TY  - JOUR
AU  - Alimpić-Aradski, Ana
AU  - Olađe Pavlović, Mariana
AU  - Janošević, Dušica
AU  - Todorović, Slađana
AU  - Gašić, Uroš
AU  - Mišić, Danijela
AU  - Pljevljakušić, Dejan
AU  - Šavikin, Katarina
AU  - Marin, Petar D.
AU  - Giweli, Abdulhmid
AU  - Duletić-Laušević, Sonja
PY  - 2023
UR  - http://www3.interscience.wiley.com/cgi-bin/jhome/5152
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6445
AB  - Introduction: The endemic species Nepeta cyrenaica Quézel & Zaffran, native to northeastern Libya, is valued as an important honey-bearing plant.

Objectives: This study was aimed to examine the micromorphology, phytochemistry, and bioactivity of in vitro-propagated N. cyrenaica for the first time.

Materials and methods: The leaf indumentum was examined using light and scanning electron microscopy and further characterised for histochemistry. The chemical composition of essential oil (EO) was performed using GC-MS analysis, while dichloromethane (DCM), methanol (ME), ethanol (ET), and aqueous (AQ) extracts were analysed using qualitative and quantitative LC/MS analyses. The antioxidant activities of EO and extracts were assessed using three parallel assays, while enzyme-inhibiting effects were evaluated against four enzymes.

Results: The leaves bear various types of glandular trichomes, with lipophilic secretion predominating. The main EO component of EO was 1,8-cineole. A considerable number of phenolics and iridoids were tentatively identified in the ME extract. Quantitative LC/MS analysis confirmed that ferulic acid, rosmarinic acid, and epigallocatechin gallate were present in the highest amount in the extracts, in which three iridoids were also quantified. Although the ME extract contained the highest amount of polyphenolics and iridoids, the DCM extract showed the best overall biological potential. Additionally, EO exerted the strongest acetylcholinesterase and tyrosinase inhibition.

Conclusion: This study demonstrated that the endemic N. cyrenaica can be efficiently grown under in vitro conditions, where it develops various glandular trichomes that are thought to secrete and/or accumulate bioactive compounds with valuable medicinal potential.
PB  - Hoboken: John Wiley and Sons
T2  - Phytochemical Analysis
T1  - Leaves micromorphology, chemical profile, and bioactivity of in vitro-propagated Nepeta cyrenaica (Lamiaceae)
IS  - 6
VL  - 34
DO  - 10.1002/pca.3257
SP  - 661
EP  - 679
ER  - 

@article{
author = "Alimpić-Aradski, Ana and Olađe Pavlović, Mariana and Janošević, Dušica and Todorović, Slađana and Gašić, Uroš and Mišić, Danijela and Pljevljakušić, Dejan and Šavikin, Katarina and Marin, Petar D. and Giweli, Abdulhmid and Duletić-Laušević, Sonja",
year = "2023",
abstract = "Introduction: The endemic species Nepeta cyrenaica Quézel & Zaffran, native to northeastern Libya, is valued as an important honey-bearing plant.

Objectives: This study was aimed to examine the micromorphology, phytochemistry, and bioactivity of in vitro-propagated N. cyrenaica for the first time.

Materials and methods: The leaf indumentum was examined using light and scanning electron microscopy and further characterised for histochemistry. The chemical composition of essential oil (EO) was performed using GC-MS analysis, while dichloromethane (DCM), methanol (ME), ethanol (ET), and aqueous (AQ) extracts were analysed using qualitative and quantitative LC/MS analyses. The antioxidant activities of EO and extracts were assessed using three parallel assays, while enzyme-inhibiting effects were evaluated against four enzymes.

Results: The leaves bear various types of glandular trichomes, with lipophilic secretion predominating. The main EO component of EO was 1,8-cineole. A considerable number of phenolics and iridoids were tentatively identified in the ME extract. Quantitative LC/MS analysis confirmed that ferulic acid, rosmarinic acid, and epigallocatechin gallate were present in the highest amount in the extracts, in which three iridoids were also quantified. Although the ME extract contained the highest amount of polyphenolics and iridoids, the DCM extract showed the best overall biological potential. Additionally, EO exerted the strongest acetylcholinesterase and tyrosinase inhibition.

Conclusion: This study demonstrated that the endemic N. cyrenaica can be efficiently grown under in vitro conditions, where it develops various glandular trichomes that are thought to secrete and/or accumulate bioactive compounds with valuable medicinal potential.",
publisher = "Hoboken: John Wiley and Sons",
journal = "Phytochemical Analysis",
title = "Leaves micromorphology, chemical profile, and bioactivity of in vitro-propagated Nepeta cyrenaica (Lamiaceae)",
number = "6",
volume = "34",
doi = "10.1002/pca.3257",
pages = "661-679"
}

Alimpić-Aradski, A., Olađe Pavlović, M., Janošević, D., Todorović, S., Gašić, U., Mišić, D., Pljevljakušić, D., Šavikin, K., Marin, P. D., Giweli, A.,& Duletić-Laušević, S.. (2023). Leaves micromorphology, chemical profile, and bioactivity of in vitro-propagated Nepeta cyrenaica (Lamiaceae). in Phytochemical Analysis
Hoboken: John Wiley and Sons., 34(6), 661-679.
https://doi.org/10.1002/pca.3257

Alimpić-Aradski A, Olađe Pavlović M, Janošević D, Todorović S, Gašić U, Mišić D, Pljevljakušić D, Šavikin K, Marin PD, Giweli A, Duletić-Laušević S. Leaves micromorphology, chemical profile, and bioactivity of in vitro-propagated Nepeta cyrenaica (Lamiaceae). in Phytochemical Analysis. 2023;34(6):661-679.
doi:10.1002/pca.3257 .

Alimpić-Aradski, Ana, Olađe Pavlović, Mariana, Janošević, Dušica, Todorović, Slađana, Gašić, Uroš, Mišić, Danijela, Pljevljakušić, Dejan, Šavikin, Katarina, Marin, Petar D., Giweli, Abdulhmid, Duletić-Laušević, Sonja, "Leaves micromorphology, chemical profile, and bioactivity of in vitro-propagated Nepeta cyrenaica (Lamiaceae)" in Phytochemical Analysis, 34, no. 6 (2023):661-679,
https://doi.org/10.1002/pca.3257 . .

TY  - DATA
AU  - Ćuković, Katarina
AU  - Todorović, Slađana
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - Bogdanović, Milica
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6214
AB  - This dataset is a product of the doctoral dissertation titled "Identification and expression analysis of genes involved in somatic embryogenesis of centaury (Centaurium erythraea Rafn.)" funded by the Ministry of Education, Science and Technological Development, Republic of Serbia (University of Belgrade, Institute for Biological Research "Siniša Stanković"). The dataset includes the transcript sequence of a newly discovered marker for early somatic embryogenesis in centaury, named CeNA1 (ID:TR23240|c0_g1_i1), as well as gene, gene promoter and corresponding CeNA1 protein sequences for seven homologs that have intact ORF.
PB  - Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade
T1  - CeNA1: the newly discovered gene marker for early somatic embryogenesis in centaury (Centaurium erythraea Rafn.) – transcript, gene, gene promoter and protein sequences
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6214
ER  - 

@misc{
author = "Ćuković, Katarina and Todorović, Slađana and Dragićević, Milan and Simonović, Ana and Bogdanović, Milica",
year = "2023",
abstract = "This dataset is a product of the doctoral dissertation titled "Identification and expression analysis of genes involved in somatic embryogenesis of centaury (Centaurium erythraea Rafn.)" funded by the Ministry of Education, Science and Technological Development, Republic of Serbia (University of Belgrade, Institute for Biological Research "Siniša Stanković"). The dataset includes the transcript sequence of a newly discovered marker for early somatic embryogenesis in centaury, named CeNA1 (ID:TR23240|c0_g1_i1), as well as gene, gene promoter and corresponding CeNA1 protein sequences for seven homologs that have intact ORF.",
publisher = "Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade",
title = "CeNA1: the newly discovered gene marker for early somatic embryogenesis in centaury (Centaurium erythraea Rafn.) – transcript, gene, gene promoter and protein sequences",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6214"
}

Ćuković, K., Todorović, S., Dragićević, M., Simonović, A.,& Bogdanović, M.. (2023). CeNA1: the newly discovered gene marker for early somatic embryogenesis in centaury (Centaurium erythraea Rafn.) – transcript, gene, gene promoter and protein sequences. 
Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade..
https://hdl.handle.net/21.15107/rcub_ibiss_6214

Ćuković K, Todorović S, Dragićević M, Simonović A, Bogdanović M. CeNA1: the newly discovered gene marker for early somatic embryogenesis in centaury (Centaurium erythraea Rafn.) – transcript, gene, gene promoter and protein sequences. 2023;.
https://hdl.handle.net/21.15107/rcub_ibiss_6214 .

Ćuković, Katarina, Todorović, Slađana, Dragićević, Milan, Simonović, Ana, Bogdanović, Milica, "CeNA1: the newly discovered gene marker for early somatic embryogenesis in centaury (Centaurium erythraea Rafn.) – transcript, gene, gene promoter and protein sequences" (2023),
https://hdl.handle.net/21.15107/rcub_ibiss_6214 .

TY  - CONF
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Ćuković, Katarina
AU  - van Arkel, Jeroen
AU  - Bosch, Dirk
AU  - Cankar, Katarina
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/6155
AB  - Root chicory (Cichorium intybus var. sativum), an industrial crop species used for the production of a fructose polymer inulin, has been shown to contain a mixture of bitter tasting sesquiterpene lactones (STLs), that are currently discarded as waste. For several STLs found in plants of the Asteraceae family including chicory, interesting bioactivities have been demonstrated, including potent anti-cancer, anti-malarial, anti-inflammatory, anti-fungal and anti-bacterial activity. This activity is mainly attributed to guaianolide STLs; in chicory the most abundant STLs are lactucin, lactucopicrin, and 8-deoxylactucin, found predominantly in their oxalated forms in the latex of the plant. Several steps in the biosynthetic pathway of these compounds have been unraveled recently. However, the enzymes involved in the formation of STL oxalates, the most abundant form of STLs in chicory, have not yet been identified. Candidate genes for the chicory oxalate-CoA ligase (CiOxL) and chicory STL oxalyl transferases (CiOxT) putatively involved in the STL-oxalate formation were identified. Next, introduction of CRISPR/Cas reagents into chicory by Agrobacterium tumefaciens-mediated stable transformation was used to inactivate gene candidates putatively involved in STL-oxalate formation, and several chicory lines with edited genes were successfully regenerated. Detailed genotyping of mutant lines revealed the presence of indels leading to frame-shift predominantly, varying from 1 to 44 base pairs in length. Detailed genotyping also confirmed previous observations that plants transformed via Agrobacterium often showed chimerism, and a mixture of different on-target edits in one plant was observed. Leaves of plants carrying mutations in CiOxL or CiOxT were characterized by LC-MS to determine changes in terpene profile. The analysis showed that the production of STLs was reduced or eliminated in leaves of several CiOxL and CiOxT4 plants. Surprisingly, not only the oxalated terpenes were reduced but also the non-oxalated STLs, perhaps due to feedback regulation or toxicity of non-oxalated forms. These results contribute to further elucidation of the STL pathway in chicory and show that Agrobacterium-mediated plant transformation with CRISPR/Cas reagents requires detailed genotyping for characterization of genome edited plants.
PB  - COST Action CA18111
C3  - Book of abstracts: 4th PlantEd Conference; 2023 Sep 18-20; Porto, Portugal
T1  - CRISPR/Cas targeted inactivation of guaianolide oxalate formation in chicory
SP  - 74
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_6155
ER  - 

@conference{
author = "Bogdanović, Milica and Todorović, Slađana and Ćuković, Katarina and van Arkel, Jeroen and Bosch, Dirk and Cankar, Katarina",
year = "2023",
abstract = "Root chicory (Cichorium intybus var. sativum), an industrial crop species used for the production of a fructose polymer inulin, has been shown to contain a mixture of bitter tasting sesquiterpene lactones (STLs), that are currently discarded as waste. For several STLs found in plants of the Asteraceae family including chicory, interesting bioactivities have been demonstrated, including potent anti-cancer, anti-malarial, anti-inflammatory, anti-fungal and anti-bacterial activity. This activity is mainly attributed to guaianolide STLs; in chicory the most abundant STLs are lactucin, lactucopicrin, and 8-deoxylactucin, found predominantly in their oxalated forms in the latex of the plant. Several steps in the biosynthetic pathway of these compounds have been unraveled recently. However, the enzymes involved in the formation of STL oxalates, the most abundant form of STLs in chicory, have not yet been identified. Candidate genes for the chicory oxalate-CoA ligase (CiOxL) and chicory STL oxalyl transferases (CiOxT) putatively involved in the STL-oxalate formation were identified. Next, introduction of CRISPR/Cas reagents into chicory by Agrobacterium tumefaciens-mediated stable transformation was used to inactivate gene candidates putatively involved in STL-oxalate formation, and several chicory lines with edited genes were successfully regenerated. Detailed genotyping of mutant lines revealed the presence of indels leading to frame-shift predominantly, varying from 1 to 44 base pairs in length. Detailed genotyping also confirmed previous observations that plants transformed via Agrobacterium often showed chimerism, and a mixture of different on-target edits in one plant was observed. Leaves of plants carrying mutations in CiOxL or CiOxT were characterized by LC-MS to determine changes in terpene profile. The analysis showed that the production of STLs was reduced or eliminated in leaves of several CiOxL and CiOxT4 plants. Surprisingly, not only the oxalated terpenes were reduced but also the non-oxalated STLs, perhaps due to feedback regulation or toxicity of non-oxalated forms. These results contribute to further elucidation of the STL pathway in chicory and show that Agrobacterium-mediated plant transformation with CRISPR/Cas reagents requires detailed genotyping for characterization of genome edited plants.",
publisher = "COST Action CA18111",
journal = "Book of abstracts: 4th PlantEd Conference; 2023 Sep 18-20; Porto, Portugal",
title = "CRISPR/Cas targeted inactivation of guaianolide oxalate formation in chicory",
pages = "74",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_6155"
}

Bogdanović, M., Todorović, S., Ćuković, K., van Arkel, J., Bosch, D.,& Cankar, K.. (2023). CRISPR/Cas targeted inactivation of guaianolide oxalate formation in chicory. in Book of abstracts: 4th PlantEd Conference; 2023 Sep 18-20; Porto, Portugal
COST Action CA18111., 74.
https://hdl.handle.net/21.15107/rcub_ibiss_6155

Bogdanović M, Todorović S, Ćuković K, van Arkel J, Bosch D, Cankar K. CRISPR/Cas targeted inactivation of guaianolide oxalate formation in chicory. in Book of abstracts: 4th PlantEd Conference; 2023 Sep 18-20; Porto, Portugal. 2023;:74.
https://hdl.handle.net/21.15107/rcub_ibiss_6155 .

Bogdanović, Milica, Todorović, Slađana, Ćuković, Katarina, van Arkel, Jeroen, Bosch, Dirk, Cankar, Katarina, "CRISPR/Cas targeted inactivation of guaianolide oxalate formation in chicory" in Book of abstracts: 4th PlantEd Conference; 2023 Sep 18-20; Porto, Portugal (2023):74,
https://hdl.handle.net/21.15107/rcub_ibiss_6155 .

TY  - JOUR
AU  - Todorović, Slađana
AU  - Perić, Marija
AU  - Nikolić, Biljana
AU  - Mandić, Boris
AU  - Cvetković, Stefana
AU  - Bogdanović, Milica
AU  - Živković, Suzana
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5795
AB  - The aim of this study was to comparatively analyze chemical composition and biological activity of wild- and in vitro grown Rindera umbellata. Explants were cultivated on 0.003–0.3 M sucrose, fructose, or glucose. HPLC-DAD for quantifying rosmarinic (RA) and lithospermic B (LAB) acids and GC-MS/FID for qualitative pyrrolizidine alkaloids (PAs) detection were used. Antioxidant activity (DPPH and ABTS assays) and cytotoxicity (MTT test) were monitored. Identified PAs were 7-angeloyl heliotridane, lindelofine, 7-angeloyl heliotridine, 7-angeloyl-9-(+)-trachelanthylheliotridine, punctanecine, and heliosupine, with higher variability reported in wild-growing samples. Total phenolic contents (TPCs) were comparable in wild-growing and in vitro samples, but total flavonoid (TFC) and RA levels were multifold higher in in vitro samples. Notably, high concentration of LAB was detected in wild-growing roots. Amounts of 0.3 M and 0.1 M of sucrose were optimal for TFC and RA production, while maximal antioxidant activity was monitored in plants grown on 0.3 M sucrose. The MTT test indicated colorectal HT-29 as more sensitive than A549 lung adenocarcinoma and normal MRC-5 cells, showing selective sensitivity to wild-growing and 0.3 M sucrose samples. In conclusion, PAs in vitro, as well as TPC, TFC, RA, and LAB in both growing conditions were detected for the first time in R. umbellata.
PB  - Basel: MDPI
T2  - Horticulturae
T1  - Chemical Characterization, Antioxidant Activity, and Cytotoxity of Wild-Growing and In Vitro Cultivated Rindera umbellata (Waldst. and Kit.) Bunge
IS  - 3
VL  - 9
DO  - 10.3390/horticulturae9030381
SP  - 381
ER  - 

@article{
author = "Todorović, Slađana and Perić, Marija and Nikolić, Biljana and Mandić, Boris and Cvetković, Stefana and Bogdanović, Milica and Živković, Suzana",
year = "2023",
abstract = "The aim of this study was to comparatively analyze chemical composition and biological activity of wild- and in vitro grown Rindera umbellata. Explants were cultivated on 0.003–0.3 M sucrose, fructose, or glucose. HPLC-DAD for quantifying rosmarinic (RA) and lithospermic B (LAB) acids and GC-MS/FID for qualitative pyrrolizidine alkaloids (PAs) detection were used. Antioxidant activity (DPPH and ABTS assays) and cytotoxicity (MTT test) were monitored. Identified PAs were 7-angeloyl heliotridane, lindelofine, 7-angeloyl heliotridine, 7-angeloyl-9-(+)-trachelanthylheliotridine, punctanecine, and heliosupine, with higher variability reported in wild-growing samples. Total phenolic contents (TPCs) were comparable in wild-growing and in vitro samples, but total flavonoid (TFC) and RA levels were multifold higher in in vitro samples. Notably, high concentration of LAB was detected in wild-growing roots. Amounts of 0.3 M and 0.1 M of sucrose were optimal for TFC and RA production, while maximal antioxidant activity was monitored in plants grown on 0.3 M sucrose. The MTT test indicated colorectal HT-29 as more sensitive than A549 lung adenocarcinoma and normal MRC-5 cells, showing selective sensitivity to wild-growing and 0.3 M sucrose samples. In conclusion, PAs in vitro, as well as TPC, TFC, RA, and LAB in both growing conditions were detected for the first time in R. umbellata.",
publisher = "Basel: MDPI",
journal = "Horticulturae",
title = "Chemical Characterization, Antioxidant Activity, and Cytotoxity of Wild-Growing and In Vitro Cultivated Rindera umbellata (Waldst. and Kit.) Bunge",
number = "3",
volume = "9",
doi = "10.3390/horticulturae9030381",
pages = "381"
}

Todorović, S., Perić, M., Nikolić, B., Mandić, B., Cvetković, S., Bogdanović, M.,& Živković, S.. (2023). Chemical Characterization, Antioxidant Activity, and Cytotoxity of Wild-Growing and In Vitro Cultivated Rindera umbellata (Waldst. and Kit.) Bunge. in Horticulturae
Basel: MDPI., 9(3), 381.
https://doi.org/10.3390/horticulturae9030381

Todorović S, Perić M, Nikolić B, Mandić B, Cvetković S, Bogdanović M, Živković S. Chemical Characterization, Antioxidant Activity, and Cytotoxity of Wild-Growing and In Vitro Cultivated Rindera umbellata (Waldst. and Kit.) Bunge. in Horticulturae. 2023;9(3):381.
doi:10.3390/horticulturae9030381 .

Todorović, Slađana, Perić, Marija, Nikolić, Biljana, Mandić, Boris, Cvetković, Stefana, Bogdanović, Milica, Živković, Suzana, "Chemical Characterization, Antioxidant Activity, and Cytotoxity of Wild-Growing and In Vitro Cultivated Rindera umbellata (Waldst. and Kit.) Bunge" in Horticulturae, 9, no. 3 (2023):381,
https://doi.org/10.3390/horticulturae9030381 . .

TY  - JOUR
AU  - Salvagnin, Umberto
AU  - Unkel, Katharina
AU  - Sprink, Thorben
AU  - Bundock, Paul
AU  - Sevenier, Robert
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Cankar, Katarina
AU  - Hakkert, Johanna Christina
AU  - Schijlen, Elio
AU  - Nieuwenhuis, Ronald
AU  - Hingsamer, Maria
AU  - Kulmer, Veronika
AU  - Kernitzkyi, Michael
AU  - Bosch, Dirk
AU  - Martens, Stefan
AU  - Malnoy, Mickael
PY  - 2023
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5794
AB  - Root chicory (Cichorium intybus L. var. sativum) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic. However, bitter tasting sesquiterpene lactones, giving chicory its known flavour, need to be removed during inulin extraction. To avoid this extraction and associated costs, recently chicory variants with a lower sesquiterpene lactone content were created by inactivating the four copies of the germacrene A synthase gene (CiGAS-S1, -S2, -S3, -L) which encode the enzyme initiating bitter sesquiterpene lactone biosynthesis in chicory. In this study, different delivery methods for CRISPR/Cas9 reagents have been compared regarding their efficiency to induce mutations in the CiGAS genes, the frequency of off-target mutations as well as their environmental and economic impacts. CRISPR/Cas9 reagents were delivered by Agrobacterium-mediated stable transformation or transient delivery by plasmid or preassembled ribonucleic complexes (RNPs) using the same sgRNA. All methods used lead to a high number of INDEL mutations within the CiGAS-S1 and CiGAS-S2 genes, which match the used sgRNA perfectly; additionally, the CiGAS-S3 and CiGAS-L genes, which have a single mismatch with the sgRNA, were mutated but with a lower mutation efficiency. While using both RNPs and plasmids delivery resulted in biallelic, heterozygous or homozygous mutations, plasmid delivery resulted in 30% of unwanted integration of plasmid fragments in the genome. Plants transformed via Agrobacteria often showed chimerism and a mixture of CiGAS genotypes. This genetic mosaic becomes more diverse when plants were grown over a prolonged period. While the genotype of the on-targets varied between the transient and stable delivery methods, no off-target activity in six identified potential off-targets with two to four mismatches was found. The environmental impacts (greenhouse gas (GHG) emissions and primary energy demand) of the methods are highly dependent on their individual electricity demand. From an economic view - like for most research and development activities - employment and value-added multiplier effects are high; particularly when compared to industrial or manufacturing processes. Considering all aspects, we conclude that using RNPs is the most suitable method for genome editing in chicory since it led to a high efficiency of editing, no off-target mutations, non-transgenic plants with no risk of unwanted integration of plasmid DNA and without needed segregation of transgenes.
PB  - Lausanne: Frontiers Media SA
T2  - Frontiers in Plant Science
T1  - A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L
VL  - 14
DO  - 10.3389/fpls.2023.1111110
SP  - 1111110
ER  - 

@article{
author = "Salvagnin, Umberto and Unkel, Katharina and Sprink, Thorben and Bundock, Paul and Sevenier, Robert and Bogdanović, Milica and Todorović, Slađana and Cankar, Katarina and Hakkert, Johanna Christina and Schijlen, Elio and Nieuwenhuis, Ronald and Hingsamer, Maria and Kulmer, Veronika and Kernitzkyi, Michael and Bosch, Dirk and Martens, Stefan and Malnoy, Mickael",
year = "2023",
abstract = "Root chicory (Cichorium intybus L. var. sativum) is used to extract inulin, a fructose polymer used as a natural sweetener and prebiotic. However, bitter tasting sesquiterpene lactones, giving chicory its known flavour, need to be removed during inulin extraction. To avoid this extraction and associated costs, recently chicory variants with a lower sesquiterpene lactone content were created by inactivating the four copies of the germacrene A synthase gene (CiGAS-S1, -S2, -S3, -L) which encode the enzyme initiating bitter sesquiterpene lactone biosynthesis in chicory. In this study, different delivery methods for CRISPR/Cas9 reagents have been compared regarding their efficiency to induce mutations in the CiGAS genes, the frequency of off-target mutations as well as their environmental and economic impacts. CRISPR/Cas9 reagents were delivered by Agrobacterium-mediated stable transformation or transient delivery by plasmid or preassembled ribonucleic complexes (RNPs) using the same sgRNA. All methods used lead to a high number of INDEL mutations within the CiGAS-S1 and CiGAS-S2 genes, which match the used sgRNA perfectly; additionally, the CiGAS-S3 and CiGAS-L genes, which have a single mismatch with the sgRNA, were mutated but with a lower mutation efficiency. While using both RNPs and plasmids delivery resulted in biallelic, heterozygous or homozygous mutations, plasmid delivery resulted in 30% of unwanted integration of plasmid fragments in the genome. Plants transformed via Agrobacteria often showed chimerism and a mixture of CiGAS genotypes. This genetic mosaic becomes more diverse when plants were grown over a prolonged period. While the genotype of the on-targets varied between the transient and stable delivery methods, no off-target activity in six identified potential off-targets with two to four mismatches was found. The environmental impacts (greenhouse gas (GHG) emissions and primary energy demand) of the methods are highly dependent on their individual electricity demand. From an economic view - like for most research and development activities - employment and value-added multiplier effects are high; particularly when compared to industrial or manufacturing processes. Considering all aspects, we conclude that using RNPs is the most suitable method for genome editing in chicory since it led to a high efficiency of editing, no off-target mutations, non-transgenic plants with no risk of unwanted integration of plasmid DNA and without needed segregation of transgenes.",
publisher = "Lausanne: Frontiers Media SA",
journal = "Frontiers in Plant Science",
title = "A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L",
volume = "14",
doi = "10.3389/fpls.2023.1111110",
pages = "1111110"
}

Salvagnin, U., Unkel, K., Sprink, T., Bundock, P., Sevenier, R., Bogdanović, M., Todorović, S., Cankar, K., Hakkert, J. C., Schijlen, E., Nieuwenhuis, R., Hingsamer, M., Kulmer, V., Kernitzkyi, M., Bosch, D., Martens, S.,& Malnoy, M.. (2023). A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L. in Frontiers in Plant Science
Lausanne: Frontiers Media SA., 14, 1111110.
https://doi.org/10.3389/fpls.2023.1111110

Salvagnin U, Unkel K, Sprink T, Bundock P, Sevenier R, Bogdanović M, Todorović S, Cankar K, Hakkert JC, Schijlen E, Nieuwenhuis R, Hingsamer M, Kulmer V, Kernitzkyi M, Bosch D, Martens S, Malnoy M. A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L. in Frontiers in Plant Science. 2023;14:1111110.
doi:10.3389/fpls.2023.1111110 .

Salvagnin, Umberto, Unkel, Katharina, Sprink, Thorben, Bundock, Paul, Sevenier, Robert, Bogdanović, Milica, Todorović, Slađana, Cankar, Katarina, Hakkert, Johanna Christina, Schijlen, Elio, Nieuwenhuis, Ronald, Hingsamer, Maria, Kulmer, Veronika, Kernitzkyi, Michael, Bosch, Dirk, Martens, Stefan, Malnoy, Mickael, "A comparison of three different delivery methods for achieving CRISPR/Cas9 mediated genome editing in Cichorium intybus L" in Frontiers in Plant Science, 14 (2023):1111110,
https://doi.org/10.3389/fpls.2023.1111110 . .

TY  - JOUR
AU  - Skorić, Marijana
AU  - Ćirić, Ana
AU  - Budimir, Snežana
AU  - Janošević, Dušica
AU  - Anđelković, Boban
AU  - Todosijević, Marina
AU  - Todorović, Slađana
AU  - Soković, Marina
AU  - Glamočlija, Jasmina
AU  - Tešević, Vele
AU  - Gašić, Uroš
AU  - Mišić, Danijela
AU  - Kanellis, Angelos K.
PY  - 2022
UR  - https://linkinghub.elsevier.com/retrieve/pii/S0926669022004757
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4983
AB  - Cistus creticus subsp. creticus is a shrubby Mediterranean plant used since ancient times in folk medicine for the treatment of different diseases. C. creticus extracts and resin contain different types of secondary metabolites , such as terpenoids (predominantly labdane type diterpenoids), and phenylpropanoids. Growth conditions seem to influence the content of labdane-type diterpenes and flavan-3-ols in leaves of C. creticus subsp. creticus . Histochemical staining of leaves' trichomes and comprehensive phytochemical characterization of resin, leaves and their exudates, indicated that long-stalked capitate trichomes of C. creticus subsp. creticus , grown both in vitro (IV) and in greenhouse (GH), are capable of producing bioactive oleoresin-related terpenoids and phenylpropanoids compounds. Bioactivity-guided approach was implemented in search for the major antibacterial compound in C. creticus resin against two Gram-negative ( Escherichia coli and Pseudomonas aeruginosa ) and two Gram-positive bacteria ( Bacillus cereus and Micrococcus flavus ). Bioautographic assay on TLC plates with separated components of Cistus resin extract, revealed a pronounced zone of microbial growth inhibition, corresponded to a highly active compound with Rf values of 0.45, structurally characterized and identified as ent -3 β -acetoxy-13- epi -manoyl oxide. This finding opens the route for focusing on isolation and functional characterization of genes involved in the biosynthesis of ent -3 β -acetoxy-13- epi -manoyl oxide and its precursor ent -3 β -hydroxy-13- epi -manoyl oxide, with the aim to establish sustainable in vitro biotechnological protocols for its large-scale production in homologous and heterologous plant and microbial hosts.
PB  - Elsevier B.V.
T2  - Industrial Crops and Products
T1  - Bioactivity-guided identification and isolation of a major antimicrobial compound in Cistus creticus subsp. creticus leaves and resin “ladano”
VL  - 184
DO  - 10.1016/j.indcrop.2022.114992
SP  - 114992
ER  - 

@article{
author = "Skorić, Marijana and Ćirić, Ana and Budimir, Snežana and Janošević, Dušica and Anđelković, Boban and Todosijević, Marina and Todorović, Slađana and Soković, Marina and Glamočlija, Jasmina and Tešević, Vele and Gašić, Uroš and Mišić, Danijela and Kanellis, Angelos K.",
year = "2022",
abstract = "Cistus creticus subsp. creticus is a shrubby Mediterranean plant used since ancient times in folk medicine for the treatment of different diseases. C. creticus extracts and resin contain different types of secondary metabolites , such as terpenoids (predominantly labdane type diterpenoids), and phenylpropanoids. Growth conditions seem to influence the content of labdane-type diterpenes and flavan-3-ols in leaves of C. creticus subsp. creticus . Histochemical staining of leaves' trichomes and comprehensive phytochemical characterization of resin, leaves and their exudates, indicated that long-stalked capitate trichomes of C. creticus subsp. creticus , grown both in vitro (IV) and in greenhouse (GH), are capable of producing bioactive oleoresin-related terpenoids and phenylpropanoids compounds. Bioactivity-guided approach was implemented in search for the major antibacterial compound in C. creticus resin against two Gram-negative ( Escherichia coli and Pseudomonas aeruginosa ) and two Gram-positive bacteria ( Bacillus cereus and Micrococcus flavus ). Bioautographic assay on TLC plates with separated components of Cistus resin extract, revealed a pronounced zone of microbial growth inhibition, corresponded to a highly active compound with Rf values of 0.45, structurally characterized and identified as ent -3 β -acetoxy-13- epi -manoyl oxide. This finding opens the route for focusing on isolation and functional characterization of genes involved in the biosynthesis of ent -3 β -acetoxy-13- epi -manoyl oxide and its precursor ent -3 β -hydroxy-13- epi -manoyl oxide, with the aim to establish sustainable in vitro biotechnological protocols for its large-scale production in homologous and heterologous plant and microbial hosts.",
publisher = "Elsevier B.V.",
journal = "Industrial Crops and Products",
title = "Bioactivity-guided identification and isolation of a major antimicrobial compound in Cistus creticus subsp. creticus leaves and resin “ladano”",
volume = "184",
doi = "10.1016/j.indcrop.2022.114992",
pages = "114992"
}

Skorić, M., Ćirić, A., Budimir, S., Janošević, D., Anđelković, B., Todosijević, M., Todorović, S., Soković, M., Glamočlija, J., Tešević, V., Gašić, U., Mišić, D.,& Kanellis, A. K.. (2022). Bioactivity-guided identification and isolation of a major antimicrobial compound in Cistus creticus subsp. creticus leaves and resin “ladano”. in Industrial Crops and Products
Elsevier B.V.., 184, 114992.
https://doi.org/10.1016/j.indcrop.2022.114992

Skorić M, Ćirić A, Budimir S, Janošević D, Anđelković B, Todosijević M, Todorović S, Soković M, Glamočlija J, Tešević V, Gašić U, Mišić D, Kanellis AK. Bioactivity-guided identification and isolation of a major antimicrobial compound in Cistus creticus subsp. creticus leaves and resin “ladano”. in Industrial Crops and Products. 2022;184:114992.
doi:10.1016/j.indcrop.2022.114992 .

Skorić, Marijana, Ćirić, Ana, Budimir, Snežana, Janošević, Dušica, Anđelković, Boban, Todosijević, Marina, Todorović, Slađana, Soković, Marina, Glamočlija, Jasmina, Tešević, Vele, Gašić, Uroš, Mišić, Danijela, Kanellis, Angelos K., "Bioactivity-guided identification and isolation of a major antimicrobial compound in Cistus creticus subsp. creticus leaves and resin “ladano”" in Industrial Crops and Products, 184 (2022):114992,
https://doi.org/10.1016/j.indcrop.2022.114992 . .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Bogdanović, Milica
AU  - Simonović, Ana
AU  - Todorović, Slađana
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5894
AB  - Описана је метода за транформацију C. erythraea сојем GV3101 А. tumefaciens, 
тестирана на одсечцима листова и врховима коренова биљака гајених in vitro. Сој 
GV3101 носи бинарни плазмид pXK7S2D који обезбеђује резистенцију на 
канамицин. Након кокултивације експлантати су преношени на серију подлога за 
регенерацију са додатком различитих регулатора растења: 1 mg·l

-1 

бензиламинопурина, 0,1 или 0,4 mg·l

-1 индол-3-сирћетне киселине и 1 mg·l-1 
кинетина. Као селекциони антибиотик коришћен је канамицин у концентрацији од 
50 mg·l

-1 за листове или 25 mg·l-1 за коренове, док су цефотаксим и ванкомицин 
концентрација 250 mg·l

-1, односно 50 mg·l-1 додавани у подлогу ради превенције 
раста бактерија. Контролни експлантати су преношени на подлоге истог састава и 
на подлогу без канамицина. Након 6 недеља на листовима су уочени спонтано 
формирани изданци, док на кореновима није запажена регенерација, чак ни на 
контролним експлантатима. Изданци формирани на листовима одсецани су, 
пребацивани на MS подлогу са 0,2 mg·l

-1 индол-3-бутерне киселине и 150 mg·l-1 
цефотаксима и гајени до потпуног формирања биљке. Регенерисане биљке су 
тестиране на присуство трансгена методом Phire PCR-a. Успешност 
трансформације износила је 17,64%. Имајући у виду да је до сада помоћу A. 
tumefaciens трансформисано само неколико биљних врста из фамилије 
Gentianaceae, описана техника за трансформацију листа нуди перспективу за даљу 
примену, нарочито на врстама рода Centaurium.
AB  - Opisana je metoda za tranformaciju C. erythraea sojem GV3101 A. tumefaciens, testirana na odsečcima listova i vrhovima korenova bilјaka gajenih in vitro. Soj GV3101 nosi binarni plazmid pXK7S2D koji obezbeđuje rezistenciju na kanamicin. Nakon kokultivacije eksplantati su prenošeni na seriju podloga za regeneraciju sa dodatkom različitih regulatora rastenja: 1 mg·l -1 benzilaminopurina, 0,1 ili 0,4 mg·l -1 indol-3-sirćetne kiseline i 1 mg·l-1 kinetina. Kao selekcioni antibiotik korišćen je kanamicin u koncentraciji od 50 mg·l -1 za listove ili 25 mg·l-1 za korenove, dok su cefotaksim i vankomicin koncentracija 250 mg·l -1, odnosno 50 mg·l-1 dodavani u podlogu radi prevencije rasta bakterija. Kontrolni eksplantati su prenošeni na podloge istog sastava i na podlogu bez kanamicina. Nakon 6 nedelјa na listovima su uočeni spontano formirani izdanci, dok na korenovima nije zapažena regeneracija, čak ni na kontrolnim eksplantatima. Izdanci formirani na listovima odsecani su, prebacivani na MS podlogu sa 0,2 mg·l -1 indol-3-buterne kiseline i 150 mg·l-1 cefotaksima i gajeni do potpunog formiranja bilјke. Regenerisane bilјke su testirane na prisustvo transgena metodom Phire PCR-a. Uspešnost transformacije iznosila je 17,64%. Imajući u vidu da je do sada pomoću A. tumefaciens transformisano samo nekoliko bilјnih vrsta iz familije Gentianaceae, opisana tehnika za transformaciju lista nudi perspektivu za dalјu primenu, naročito na vrstama roda Centaurium.
PB  - Belgrade: Serbian Biological Society
C3  - Knjiga sažetaka: Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia
T1  - Генетичка трансформација листа и корена кичице (Centaurium erythraea) GV3101 сојем A. tumefaciens
T1  - Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens
SP  - 58
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5894
ER  - 

@conference{
author = "Ćuković, Katarina and Bogdanović, Milica and Simonović, Ana and Todorović, Slađana",
year = "2022",
abstract = "Описана је метода за транформацију C. erythraea сојем GV3101 А. tumefaciens, 
тестирана на одсечцима листова и врховима коренова биљака гајених in vitro. Сој 
GV3101 носи бинарни плазмид pXK7S2D који обезбеђује резистенцију на 
канамицин. Након кокултивације експлантати су преношени на серију подлога за 
регенерацију са додатком различитих регулатора растења: 1 mg·l

-1 

бензиламинопурина, 0,1 или 0,4 mg·l

-1 индол-3-сирћетне киселине и 1 mg·l-1 
кинетина. Као селекциони антибиотик коришћен је канамицин у концентрацији од 
50 mg·l

-1 за листове или 25 mg·l-1 за коренове, док су цефотаксим и ванкомицин 
концентрација 250 mg·l

-1, односно 50 mg·l-1 додавани у подлогу ради превенције 
раста бактерија. Контролни експлантати су преношени на подлоге истог састава и 
на подлогу без канамицина. Након 6 недеља на листовима су уочени спонтано 
формирани изданци, док на кореновима није запажена регенерација, чак ни на 
контролним експлантатима. Изданци формирани на листовима одсецани су, 
пребацивани на MS подлогу са 0,2 mg·l

-1 индол-3-бутерне киселине и 150 mg·l-1 
цефотаксима и гајени до потпуног формирања биљке. Регенерисане биљке су 
тестиране на присуство трансгена методом Phire PCR-a. Успешност 
трансформације износила је 17,64%. Имајући у виду да је до сада помоћу A. 
tumefaciens трансформисано само неколико биљних врста из фамилије 
Gentianaceae, описана техника за трансформацију листа нуди перспективу за даљу 
примену, нарочито на врстама рода Centaurium., Opisana je metoda za tranformaciju C. erythraea sojem GV3101 A. tumefaciens, testirana na odsečcima listova i vrhovima korenova bilјaka gajenih in vitro. Soj GV3101 nosi binarni plazmid pXK7S2D koji obezbeđuje rezistenciju na kanamicin. Nakon kokultivacije eksplantati su prenošeni na seriju podloga za regeneraciju sa dodatkom različitih regulatora rastenja: 1 mg·l -1 benzilaminopurina, 0,1 ili 0,4 mg·l -1 indol-3-sirćetne kiseline i 1 mg·l-1 kinetina. Kao selekcioni antibiotik korišćen je kanamicin u koncentraciji od 50 mg·l -1 za listove ili 25 mg·l-1 za korenove, dok su cefotaksim i vankomicin koncentracija 250 mg·l -1, odnosno 50 mg·l-1 dodavani u podlogu radi prevencije rasta bakterija. Kontrolni eksplantati su prenošeni na podloge istog sastava i na podlogu bez kanamicina. Nakon 6 nedelјa na listovima su uočeni spontano formirani izdanci, dok na korenovima nije zapažena regeneracija, čak ni na kontrolnim eksplantatima. Izdanci formirani na listovima odsecani su, prebacivani na MS podlogu sa 0,2 mg·l -1 indol-3-buterne kiseline i 150 mg·l-1 cefotaksima i gajeni do potpunog formiranja bilјke. Regenerisane bilјke su testirane na prisustvo transgena metodom Phire PCR-a. Uspešnost transformacije iznosila je 17,64%. Imajući u vidu da je do sada pomoću A. tumefaciens transformisano samo nekoliko bilјnih vrsta iz familije Gentianaceae, opisana tehnika za transformaciju lista nudi perspektivu za dalјu primenu, naročito na vrstama roda Centaurium.",
publisher = "Belgrade: Serbian Biological Society",
journal = "Knjiga sažetaka: Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia",
title = "Генетичка трансформација листа и корена кичице (Centaurium erythraea) GV3101 сојем A. tumefaciens, Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens",
pages = "58",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5894"
}

Ćuković, K., Bogdanović, M., Simonović, A.,& Todorović, S.. (2022). Генетичка трансформација листа и корена кичице (Centaurium erythraea) GV3101 сојем A. tumefaciens. in Knjiga sažetaka: Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia
Belgrade: Serbian Biological Society., 58.
https://hdl.handle.net/21.15107/rcub_ibiss_5894

Ćuković K, Bogdanović M, Simonović A, Todorović S. Генетичка трансформација листа и корена кичице (Centaurium erythraea) GV3101 сојем A. tumefaciens. in Knjiga sažetaka: Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia. 2022;:58.
https://hdl.handle.net/21.15107/rcub_ibiss_5894 .

Ćuković, Katarina, Bogdanović, Milica, Simonović, Ana, Todorović, Slađana, "Генетичка трансформација листа и корена кичице (Centaurium erythraea) GV3101 сојем A. tumefaciens" in Knjiga sažetaka: Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia (2022):58,
https://hdl.handle.net/21.15107/rcub_ibiss_5894 .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Bogdanović, Milica
AU  - Simonović, Ana
AU  - Todorović, Slađana
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5720
AB  - Описана је метода за транформацију C. erythraea сојем GV3101 А. tumefaciens, тестирана на одсечцима листова и врховима коренова биљака гајених in vitro. Сој GV3101 носи бинарни плазмид pXK7S2D који обезбеђује резистенцију на канамицин. Након кокултивације експлантати су преношени на серију подлога за регенерацију са додатком различитих регулатора растења: 1 mg·l-1 бензиламинопурина, 0.1 или 0.4 mg·l-1 индол-3-сирћетне киселине и 1 mg·l-1 кинетина. Као селекциони антибиотик коришћен је канамицин у концентрацији од 50 mg·l-1 за листове или 25 mg·l-1 за коренове, док су цефотаксим и ванкомицин концентрација 250 mg·l-1, односно 50 mg·l-1 додавани у подлогу ради превенције раста бактерија. Контролни експлантати су преношени на подлоге истог састава и на подлогу без канамицина. Након 6 недеља на листовима су уочени спонтано формирани изданци, док на кореновима није запажена регенерација, чак ни на контролним експлантатима. Изданци формирани на листовима одсецани су, пребацивани на MS подлогу са 0.2 mg·l-1 индол-3-бутерне киселине и 150 mg·l-1 цефотаксима и гајени до потпуног формирања биљке. Регенерисане биљке су тестиране на присуство трансгена методом Phire PCR-a.  Успешност трансформације износила је 17.64%. Имајући у виду да је до сада помоћу A. tumefaciens трансформисано само неколико биљних врста из фамилије Gentianaceae, описана техника за трансформацију листа нуди перспективу за даљу примену, нарочито на врстама рода Centaurium.
AB  - Opisana je metoda za tranformaciju C. erythraea sojem GV3101 A. tumefaciens, testirana na odsečcima listova i vrhovima korenova biljaka gajenih in vitro. Soj GV3101 nosi binarni plazmid pXK7S2D koji obezbeđuje rezistenciju na kanamicin. Nakon kokultivacije eksplantati su prenošeni na seriju podloga za regeneraciju sa dodatkom različitih regulatora rastenja: 1 mg·l-1 benzilaminopurina, 0.1 ili 0.4 mg·l-1 indol-3-sirćetne kiseline i 1 mg·l-1 kinetina. Kao selekcioni antibiotik korišćen je kanamicin u koncentraciji od 50 mg·l-1 za listove ili 25 mg·l-1 za korenove, dok su cefotaksim i vankomicin koncentracija 250 mg·l-1, odnosno 50 mg·l-1 dodavani u podlogu radi prevencije rasta bakterija. Kontrolni eksplantati su prenošeni na podloge istog sastava i na podlogu bez kanamicina. Nakon 6 nedelja na listovima su uočeni spontano formirani izdanci, dok na korenovima nije zapažena regeneracija, čak ni na kontrolnim eksplantatima. Izdanci formirani na listovima odsecani su, prebacivani na MS podlogu sa 0.2 mg·l-1 indol-3-buterne kiseline i 150 mg·l-1 cefotaksima i gajeni do potpunog formiranja biljke. Regenerisane biljke su testirane na prisustvo transgena metodom Phire PCR-a. Uspešnost transformacije iznosila je 17.64%. Imajući u vidu da je do sada pomoću A. tumefaciens transformisano samo nekoliko biljnih vrsta iz familije Gentianaceae, opisana tehnika za transformaciju lista nudi perspektivu za dalju primenu, naročito na vrstama roda Centaurium.
PB  - Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade
C3  - (poster) Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia
T1  - Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens
T1  - Генетичка трансформација листа и корена кичице (Centaurium erythraea) помоћу GV3101 соја A. tumefaciens
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5720
ER  - 

@conference{
author = "Ćuković, Katarina and Bogdanović, Milica and Simonović, Ana and Todorović, Slađana",
year = "2022",
abstract = "Описана је метода за транформацију C. erythraea сојем GV3101 А. tumefaciens, тестирана на одсечцима листова и врховима коренова биљака гајених in vitro. Сој GV3101 носи бинарни плазмид pXK7S2D који обезбеђује резистенцију на канамицин. Након кокултивације експлантати су преношени на серију подлога за регенерацију са додатком различитих регулатора растења: 1 mg·l-1 бензиламинопурина, 0.1 или 0.4 mg·l-1 индол-3-сирћетне киселине и 1 mg·l-1 кинетина. Као селекциони антибиотик коришћен је канамицин у концентрацији од 50 mg·l-1 за листове или 25 mg·l-1 за коренове, док су цефотаксим и ванкомицин концентрација 250 mg·l-1, односно 50 mg·l-1 додавани у подлогу ради превенције раста бактерија. Контролни експлантати су преношени на подлоге истог састава и на подлогу без канамицина. Након 6 недеља на листовима су уочени спонтано формирани изданци, док на кореновима није запажена регенерација, чак ни на контролним експлантатима. Изданци формирани на листовима одсецани су, пребацивани на MS подлогу са 0.2 mg·l-1 индол-3-бутерне киселине и 150 mg·l-1 цефотаксима и гајени до потпуног формирања биљке. Регенерисане биљке су тестиране на присуство трансгена методом Phire PCR-a.  Успешност трансформације износила је 17.64%. Имајући у виду да је до сада помоћу A. tumefaciens трансформисано само неколико биљних врста из фамилије Gentianaceae, описана техника за трансформацију листа нуди перспективу за даљу примену, нарочито на врстама рода Centaurium., Opisana je metoda za tranformaciju C. erythraea sojem GV3101 A. tumefaciens, testirana na odsečcima listova i vrhovima korenova biljaka gajenih in vitro. Soj GV3101 nosi binarni plazmid pXK7S2D koji obezbeđuje rezistenciju na kanamicin. Nakon kokultivacije eksplantati su prenošeni na seriju podloga za regeneraciju sa dodatkom različitih regulatora rastenja: 1 mg·l-1 benzilaminopurina, 0.1 ili 0.4 mg·l-1 indol-3-sirćetne kiseline i 1 mg·l-1 kinetina. Kao selekcioni antibiotik korišćen je kanamicin u koncentraciji od 50 mg·l-1 za listove ili 25 mg·l-1 za korenove, dok su cefotaksim i vankomicin koncentracija 250 mg·l-1, odnosno 50 mg·l-1 dodavani u podlogu radi prevencije rasta bakterija. Kontrolni eksplantati su prenošeni na podloge istog sastava i na podlogu bez kanamicina. Nakon 6 nedelja na listovima su uočeni spontano formirani izdanci, dok na korenovima nije zapažena regeneracija, čak ni na kontrolnim eksplantatima. Izdanci formirani na listovima odsecani su, prebacivani na MS podlogu sa 0.2 mg·l-1 indol-3-buterne kiseline i 150 mg·l-1 cefotaksima i gajeni do potpunog formiranja biljke. Regenerisane biljke su testirane na prisustvo transgena metodom Phire PCR-a. Uspešnost transformacije iznosila je 17.64%. Imajući u vidu da je do sada pomoću A. tumefaciens transformisano samo nekoliko biljnih vrsta iz familije Gentianaceae, opisana tehnika za transformaciju lista nudi perspektivu za dalju primenu, naročito na vrstama roda Centaurium.",
publisher = "Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade",
journal = "(poster) Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia",
title = "Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens, Генетичка трансформација листа и корена кичице (Centaurium erythraea) помоћу GV3101 соја A. tumefaciens",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5720"
}

Ćuković, K., Bogdanović, M., Simonović, A.,& Todorović, S.. (2022). Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens. in (poster) Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia
Belgrade: Institute for Biological Research "Siniša Stanković"– National Institute of Republic of Serbia, University of Belgrade..
https://hdl.handle.net/21.15107/rcub_ibiss_5720

Ćuković K, Bogdanović M, Simonović A, Todorović S. Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens. in (poster) Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia. 2022;.
https://hdl.handle.net/21.15107/rcub_ibiss_5720 .

Ćuković, Katarina, Bogdanović, Milica, Simonović, Ana, Todorović, Slađana, "Genetička transformacija lista i korena kičice (Centaurium erythraea) GV3101 sojem A. tumefaciens" in (poster) Treći Kongres biologa Srbije: Osnovna i primenjena istraživanja: Metodika nastave; 2022 Sep 21-25; Zlatibor, Serbia (2022),
https://hdl.handle.net/21.15107/rcub_ibiss_5720 .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Bogdanović, Milica
AU  - Simonović, Ana
AU  - Todorović, Slađana
PY  - 2022
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5328
AB  - A genetic transformation method via secondary somatic embryogenesis is described for Centaurium erythraea. Cotyledonary somatic embryos (cse) induced on leaf explants were used for inoculation with A. tumefaciens strain GV3101 containing the binary vector pXK7S2D that provides kanamycin resistance. Inoculated embryos were cultured on MS medium enriched with 2,4-dichlorophenoxyacetic acid and N-(2-chloro-4-pyridyl)-N’-phenylurea that promote somatic embryogenesis, with addition of acetosyringone. Cse were transferred on induction medium supplemented with cefotaxime and 5 or 10 mg/L kanamycin for selection. Embryogenic tissue, induced on primary cse explants during the selection period in the dark, was transferred to hormone-free medium maintaining the same antibiotic combination. Morphologically normal secondary cse that survived kanamycin exposure were isolated and subcultured on hormone-free medium containing cefotaxime and IBA to enhance germination. Fully regenerated plants were analyzed by Phire PCR to determine the transgene presence. Transformation efficiency was higher on media with 10 mg/L kanamycin (17.64%) as compared to 6.67% efficiency obtained on 5 mg/L. To the best of our knowledge, this is the first report on centaury transformation via secondary somatic embryogenesis, which offers an alternative to leaf or root explant transformation and provides an additional tool for investigating in vitro developmental pathways in this plant species.
PB  - Niš : Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš
PB  - Belgrade : Institute for Nature Conservation of Serbia
C3  - Abstracts: 14th Symposium on the flora of southeastern Serbia and neighboring regions; 2022 Jun 26-29; Kladovo, Serbia
T1  - An efficient  Agrobacterium tumefaciens - mediated genetic transformation method for Centaurium erythraea via secondary somatic embrygenesis
SP  - 112
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5328
ER  - 

@conference{
author = "Ćuković, Katarina and Bogdanović, Milica and Simonović, Ana and Todorović, Slađana",
year = "2022",
abstract = "A genetic transformation method via secondary somatic embryogenesis is described for Centaurium erythraea. Cotyledonary somatic embryos (cse) induced on leaf explants were used for inoculation with A. tumefaciens strain GV3101 containing the binary vector pXK7S2D that provides kanamycin resistance. Inoculated embryos were cultured on MS medium enriched with 2,4-dichlorophenoxyacetic acid and N-(2-chloro-4-pyridyl)-N’-phenylurea that promote somatic embryogenesis, with addition of acetosyringone. Cse were transferred on induction medium supplemented with cefotaxime and 5 or 10 mg/L kanamycin for selection. Embryogenic tissue, induced on primary cse explants during the selection period in the dark, was transferred to hormone-free medium maintaining the same antibiotic combination. Morphologically normal secondary cse that survived kanamycin exposure were isolated and subcultured on hormone-free medium containing cefotaxime and IBA to enhance germination. Fully regenerated plants were analyzed by Phire PCR to determine the transgene presence. Transformation efficiency was higher on media with 10 mg/L kanamycin (17.64%) as compared to 6.67% efficiency obtained on 5 mg/L. To the best of our knowledge, this is the first report on centaury transformation via secondary somatic embryogenesis, which offers an alternative to leaf or root explant transformation and provides an additional tool for investigating in vitro developmental pathways in this plant species.",
publisher = "Niš : Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš, Belgrade : Institute for Nature Conservation of Serbia",
journal = "Abstracts: 14th Symposium on the flora of southeastern Serbia and neighboring regions; 2022 Jun 26-29; Kladovo, Serbia",
title = "An efficient  Agrobacterium tumefaciens - mediated genetic transformation method for Centaurium erythraea via secondary somatic embrygenesis",
pages = "112",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5328"
}

Ćuković, K., Bogdanović, M., Simonović, A.,& Todorović, S.. (2022). An efficient  Agrobacterium tumefaciens - mediated genetic transformation method for Centaurium erythraea via secondary somatic embrygenesis. in Abstracts: 14th Symposium on the flora of southeastern Serbia and neighboring regions; 2022 Jun 26-29; Kladovo, Serbia
Niš : Department of Biology and Ecology, Faculty of Sciences and Mathematics, University of Niš., 112.
https://hdl.handle.net/21.15107/rcub_ibiss_5328

Ćuković K, Bogdanović M, Simonović A, Todorović S. An efficient  Agrobacterium tumefaciens - mediated genetic transformation method for Centaurium erythraea via secondary somatic embrygenesis. in Abstracts: 14th Symposium on the flora of southeastern Serbia and neighboring regions; 2022 Jun 26-29; Kladovo, Serbia. 2022;:112.
https://hdl.handle.net/21.15107/rcub_ibiss_5328 .

Ćuković, Katarina, Bogdanović, Milica, Simonović, Ana, Todorović, Slađana, "An efficient  Agrobacterium tumefaciens - mediated genetic transformation method for Centaurium erythraea via secondary somatic embrygenesis" in Abstracts: 14th Symposium on the flora of southeastern Serbia and neighboring regions; 2022 Jun 26-29; Kladovo, Serbia (2022):112,
https://hdl.handle.net/21.15107/rcub_ibiss_5328 .

TY  - JOUR
AU  - Bogdanović, Milica
AU  - Ćuković, Katarina
AU  - Subotić, Angelina
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - Filipović, Biljana
AU  - Todorović, Slađana
PY  - 2021
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4126
AB  - Somatic embryogenesis (SE) is a developmental process during which plant somatic cells, under suitable conditions, produce embryogenic cells that develop into somatic embryos (se). SE is the most important method for plant propagation in vitro, having both fundamental and applicative significance. SE can be induced from different tissues and organs, but when se are used as explants, the process is recognized as secondary or cyclic SE. We induced secondary SE in Centaurium erythraea by application of 2,4-dichlorophenoxyacetic acid (2,4-D) and N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU). A medium containing 0.1 mgL−1 2,4-D and 0.25 mgL−1 CPPU was optimal in terms of the number of primary SE explants forming se, the number of well-developed se per explant, and morphological appearance of the obtained se. These concentrations allowed SE to progress through three cycles, whereas at higher concentrations of 0.2 mgL−1 2,4-D and 0.5 mgL−1 CPPU, only two cycles were achieved. Histological analysis revealed that secondary se are formed both directly and indirectly. Secondary SE readily germinated and converted into plantlets. Induction of cyclic SE contributes to the conservation efforts of this endangered medicinal plant and expands the spectrum of in vitro developmental pathways described in centaury—an emerging model in developmental biology.
PB  - Basel : MDPI
T2  - Plants
T1  - Secondary Somatic Embryogenesis in Centaurium erythraea Rafn
IS  - 2
VL  - 10
DO  - 10.3390/plants10020199
SP  - 199
ER  - 

@article{
author = "Bogdanović, Milica and Ćuković, Katarina and Subotić, Angelina and Dragićević, Milan and Simonović, Ana and Filipović, Biljana and Todorović, Slađana",
year = "2021",
abstract = "Somatic embryogenesis (SE) is a developmental process during which plant somatic cells, under suitable conditions, produce embryogenic cells that develop into somatic embryos (se). SE is the most important method for plant propagation in vitro, having both fundamental and applicative significance. SE can be induced from different tissues and organs, but when se are used as explants, the process is recognized as secondary or cyclic SE. We induced secondary SE in Centaurium erythraea by application of 2,4-dichlorophenoxyacetic acid (2,4-D) and N-(2-chloro-4-pyridyl)-N′-phenylurea (CPPU). A medium containing 0.1 mgL−1 2,4-D and 0.25 mgL−1 CPPU was optimal in terms of the number of primary SE explants forming se, the number of well-developed se per explant, and morphological appearance of the obtained se. These concentrations allowed SE to progress through three cycles, whereas at higher concentrations of 0.2 mgL−1 2,4-D and 0.5 mgL−1 CPPU, only two cycles were achieved. Histological analysis revealed that secondary se are formed both directly and indirectly. Secondary SE readily germinated and converted into plantlets. Induction of cyclic SE contributes to the conservation efforts of this endangered medicinal plant and expands the spectrum of in vitro developmental pathways described in centaury—an emerging model in developmental biology.",
publisher = "Basel : MDPI",
journal = "Plants",
title = "Secondary Somatic Embryogenesis in Centaurium erythraea Rafn",
number = "2",
volume = "10",
doi = "10.3390/plants10020199",
pages = "199"
}

Bogdanović, M., Ćuković, K., Subotić, A., Dragićević, M., Simonović, A., Filipović, B.,& Todorović, S.. (2021). Secondary Somatic Embryogenesis in Centaurium erythraea Rafn. in Plants
Basel : MDPI., 10(2), 199.
https://doi.org/10.3390/plants10020199

Bogdanović M, Ćuković K, Subotić A, Dragićević M, Simonović A, Filipović B, Todorović S. Secondary Somatic Embryogenesis in Centaurium erythraea Rafn. in Plants. 2021;10(2):199.
doi:10.3390/plants10020199 .

Bogdanović, Milica, Ćuković, Katarina, Subotić, Angelina, Dragićević, Milan, Simonović, Ana, Filipović, Biljana, Todorović, Slađana, "Secondary Somatic Embryogenesis in Centaurium erythraea Rafn" in Plants, 10, no. 2 (2021):199,
https://doi.org/10.3390/plants10020199 . .

TY  - JOUR
AU  - Paunović, Danijela
AU  - Ćuković, Katarina
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Trifunović-Momčilov, Milana
AU  - Subotić, Angelina
AU  - Simonović, Ana
AU  - Dragićević, Milan
PY  - 2021
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4392
AB  - Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.
PB  - Basel: MDPI
T2  - Plants
T1  - The Arabinogalactan Protein Family of Centaurium erythraea Rafn
IS  - 9
VL  - 10
DO  - 10.3390/plants10091870
SP  - 1870
ER  - 

@article{
author = "Paunović, Danijela and Ćuković, Katarina and Bogdanović, Milica and Todorović, Slađana and Trifunović-Momčilov, Milana and Subotić, Angelina and Simonović, Ana and Dragićević, Milan",
year = "2021",
abstract = "Centaurium erythraea (centaury) is a medicinal plant with exceptional developmental plasticity in vitro and vigorous, often spontaneous, regeneration via shoot organogenesis and somatic embryogenesis, during which arabinogalactan proteins (AGPs) play an important role. AGPs are highly glycosylated proteins belonging to the super family of O-glycosylated plant cell surface hydroxyproline-rich glycoproteins (HRGPs). HRGPs/AGPs are intrinsically disordered and not well conserved, making their homology-based mining ineffective. We have applied a recently developed pipeline for HRGP/AGP mining, ragp, which is based on machine learning prediction of proline hydroxylation, to identify HRGP sequences in centaury transcriptome and to classify them into motif and amino acid bias (MAAB) classes. AGP sequences with low AG glycomotif representation were also identified. Six members of each of the three AGP subclasses, fasciclin-like AGPs, receptor kinase-like AGPs and AG peptides, were selected for phylogenetic and expression analyses. The expression of these 18 genes was recorded over 48 h following leaf mechanical wounding, as well as in 16 tissue samples representing plants from nature, plants cultivated in vitro, and developmental stages during shoot organogenesis and somatic embryogenesis. None of the selected genes were upregulated during both wounding recovery and regeneration. Possible functions of AGPs with the most interesting expression profiles are discussed.",
publisher = "Basel: MDPI",
journal = "Plants",
title = "The Arabinogalactan Protein Family of Centaurium erythraea Rafn",
number = "9",
volume = "10",
doi = "10.3390/plants10091870",
pages = "1870"
}

Paunović, D., Ćuković, K., Bogdanović, M., Todorović, S., Trifunović-Momčilov, M., Subotić, A., Simonović, A.,& Dragićević, M.. (2021). The Arabinogalactan Protein Family of Centaurium erythraea Rafn. in Plants
Basel: MDPI., 10(9), 1870.
https://doi.org/10.3390/plants10091870

Paunović D, Ćuković K, Bogdanović M, Todorović S, Trifunović-Momčilov M, Subotić A, Simonović A, Dragićević M. The Arabinogalactan Protein Family of Centaurium erythraea Rafn. in Plants. 2021;10(9):1870.
doi:10.3390/plants10091870 .

Paunović, Danijela, Ćuković, Katarina, Bogdanović, Milica, Todorović, Slađana, Trifunović-Momčilov, Milana, Subotić, Angelina, Simonović, Ana, Dragićević, Milan, "The Arabinogalactan Protein Family of Centaurium erythraea Rafn" in Plants, 10, no. 9 (2021):1870,
https://doi.org/10.3390/plants10091870 . .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Todorović, Slađana
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - Bogdanović, Milica
PY  - 2021
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4889
AB  - Centaurium erythraea Rafn is medically significant plant with a great potential in treating multiple gastrointestinal tract diseases. Although widely spread, C. erythraea is now listed as endangered species due to extensive exploitation, so there is a need to deepen knowledge of existing and developnew in vitro techniques for its mass propagation. Somatic embryogenesis (SE) is the most effective way for centaury in vitro regeneration. In addition to possessing great multiplication rate, regeneration via SE is also convenient for genetic transformation since somatic embryos offer genetically uniform starting material with less somaclonal variability. Furthermore, the ability of somatic embryos to undergo secondary SE, a process in which new somatic embryos are initiated from somatic embryos, makes them a suitable target tissue for transformation. We have recently established secondary SE in C. erythraea for the first time and our next step is to develop a transformation method using somatic embryos as starting material. Choice of the correct type and optimal concentration of decontamination and selection antibiotics is crucial in order to obtaina high germination rate and normal morphology of somatic embryos as a prerequisite for successful transformation. Therefore, we evaluated antibiotic sensitivity of untransformed somatic embryos, using different concentrations of cefotaxime and kanamycin as decontamination and selection antibiotics, respectively, and appropriate concentrations were determined. These conclusions were furthermore verified by visual observations of secondary somatic embryos number, their morphology as well as germination rate of embryos grown on media containing various antibiotics concentrations.
PB  - East Sarajevo: Faculty of Agriculture
T1  - Evaluation of kanamycin and cefotaxime effects on proliferation, morphology and germination rate of somatic embryos in Centaurium erythraea Rafn
SP  - 215
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4889
ER  - 

@conference{
author = "Ćuković, Katarina and Todorović, Slađana and Dragićević, Milan and Simonović, Ana and Bogdanović, Milica",
year = "2021",
abstract = "Centaurium erythraea Rafn is medically significant plant with a great potential in treating multiple gastrointestinal tract diseases. Although widely spread, C. erythraea is now listed as endangered species due to extensive exploitation, so there is a need to deepen knowledge of existing and developnew in vitro techniques for its mass propagation. Somatic embryogenesis (SE) is the most effective way for centaury in vitro regeneration. In addition to possessing great multiplication rate, regeneration via SE is also convenient for genetic transformation since somatic embryos offer genetically uniform starting material with less somaclonal variability. Furthermore, the ability of somatic embryos to undergo secondary SE, a process in which new somatic embryos are initiated from somatic embryos, makes them a suitable target tissue for transformation. We have recently established secondary SE in C. erythraea for the first time and our next step is to develop a transformation method using somatic embryos as starting material. Choice of the correct type and optimal concentration of decontamination and selection antibiotics is crucial in order to obtaina high germination rate and normal morphology of somatic embryos as a prerequisite for successful transformation. Therefore, we evaluated antibiotic sensitivity of untransformed somatic embryos, using different concentrations of cefotaxime and kanamycin as decontamination and selection antibiotics, respectively, and appropriate concentrations were determined. These conclusions were furthermore verified by visual observations of secondary somatic embryos number, their morphology as well as germination rate of embryos grown on media containing various antibiotics concentrations.",
publisher = "East Sarajevo: Faculty of Agriculture",
title = "Evaluation of kanamycin and cefotaxime effects on proliferation, morphology and germination rate of somatic embryos in Centaurium erythraea Rafn",
pages = "215",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4889"
}

Ćuković, K., Todorović, S., Dragićević, M., Simonović, A.,& Bogdanović, M.. (2021). Evaluation of kanamycin and cefotaxime effects on proliferation, morphology and germination rate of somatic embryos in Centaurium erythraea Rafn. 
East Sarajevo: Faculty of Agriculture., 215.
https://hdl.handle.net/21.15107/rcub_ibiss_4889

Ćuković K, Todorović S, Dragićević M, Simonović A, Bogdanović M. Evaluation of kanamycin and cefotaxime effects on proliferation, morphology and germination rate of somatic embryos in Centaurium erythraea Rafn. 2021;:215.
https://hdl.handle.net/21.15107/rcub_ibiss_4889 .

Ćuković, Katarina, Todorović, Slađana, Dragićević, Milan, Simonović, Ana, Bogdanović, Milica, "Evaluation of kanamycin and cefotaxime effects on proliferation, morphology and germination rate of somatic embryos in Centaurium erythraea Rafn" (2021):215,
https://hdl.handle.net/21.15107/rcub_ibiss_4889 .

TY  - CONF
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Beekwilder, Jules
AU  - Cankar, Katarina
AU  - Simonović, Ana
PY  - 2020
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5438
AB  - Chicory (Cichorium intybus L.) is a valuable crop grown mostly in northern France, Belgium and the Netherlands, whose roots, leaves and etiolated shoots are used as vegetable, coffee replacement and remedy for several conditions including inflammation. Roots of chicory are an important source of inulin, a prebiotic fiber and a sweetener. Chicory also contains bioactive terpene compounds that protect the plant against herbivores, but are also responsible for medicinal properties of the plant, as they have anti-microbial, anti-cancer and anti-inflammatory activity. Biosynthesis of plant bioactive metabolites can be modified using new plant breeding techniques, especially new gene editing techniques like CRISPR/Cas9 to improve their health-promoting qualities. Chicory was transformed with Agrobacterium tumefaciens carrying CRISPR/Cas9 constructs to knock-out expression of key genes in the sesquiterpene biosynthesis pathway. Regenerated plants were selected on media with kanamycin and further tested by PCR for the presence of transgenes. Obtained plants were also tested for mutations in target genes, by PCR with primers surrounding the mutation site detecting larger indels and by Sanger sequencing detecting smaller indels. Further analysis was performed detecting heteroduplex DNA fragments as a result of either hetero- or homozygous mutation events.
PB  - East Sarajevo: Faculty of Agriculture
C3  - Book of abstracts: XI International Scientific Agriculture Symposium: Agrosym 2020; 2020 Oct 8-9; Jahorina, Republika Srpska, Bosnia and Herzegovina
T1  - Metabolic engeneering in chicory by CRISPR/Cas9 editing
SP  - 152
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5438
ER  - 

@conference{
author = "Bogdanović, Milica and Todorović, Slađana and Ćuković, Katarina and Dragićević, Milan and Beekwilder, Jules and Cankar, Katarina and Simonović, Ana",
year = "2020",
abstract = "Chicory (Cichorium intybus L.) is a valuable crop grown mostly in northern France, Belgium and the Netherlands, whose roots, leaves and etiolated shoots are used as vegetable, coffee replacement and remedy for several conditions including inflammation. Roots of chicory are an important source of inulin, a prebiotic fiber and a sweetener. Chicory also contains bioactive terpene compounds that protect the plant against herbivores, but are also responsible for medicinal properties of the plant, as they have anti-microbial, anti-cancer and anti-inflammatory activity. Biosynthesis of plant bioactive metabolites can be modified using new plant breeding techniques, especially new gene editing techniques like CRISPR/Cas9 to improve their health-promoting qualities. Chicory was transformed with Agrobacterium tumefaciens carrying CRISPR/Cas9 constructs to knock-out expression of key genes in the sesquiterpene biosynthesis pathway. Regenerated plants were selected on media with kanamycin and further tested by PCR for the presence of transgenes. Obtained plants were also tested for mutations in target genes, by PCR with primers surrounding the mutation site detecting larger indels and by Sanger sequencing detecting smaller indels. Further analysis was performed detecting heteroduplex DNA fragments as a result of either hetero- or homozygous mutation events.",
publisher = "East Sarajevo: Faculty of Agriculture",
journal = "Book of abstracts: XI International Scientific Agriculture Symposium: Agrosym 2020; 2020 Oct 8-9; Jahorina, Republika Srpska, Bosnia and Herzegovina",
title = "Metabolic engeneering in chicory by CRISPR/Cas9 editing",
pages = "152",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5438"
}

Bogdanović, M., Todorović, S., Ćuković, K., Dragićević, M., Beekwilder, J., Cankar, K.,& Simonović, A.. (2020). Metabolic engeneering in chicory by CRISPR/Cas9 editing. in Book of abstracts: XI International Scientific Agriculture Symposium: Agrosym 2020; 2020 Oct 8-9; Jahorina, Republika Srpska, Bosnia and Herzegovina
East Sarajevo: Faculty of Agriculture., 152.
https://hdl.handle.net/21.15107/rcub_ibiss_5438

Bogdanović M, Todorović S, Ćuković K, Dragićević M, Beekwilder J, Cankar K, Simonović A. Metabolic engeneering in chicory by CRISPR/Cas9 editing. in Book of abstracts: XI International Scientific Agriculture Symposium: Agrosym 2020; 2020 Oct 8-9; Jahorina, Republika Srpska, Bosnia and Herzegovina. 2020;:152.
https://hdl.handle.net/21.15107/rcub_ibiss_5438 .

Bogdanović, Milica, Todorović, Slađana, Ćuković, Katarina, Dragićević, Milan, Beekwilder, Jules, Cankar, Katarina, Simonović, Ana, "Metabolic engeneering in chicory by CRISPR/Cas9 editing" in Book of abstracts: XI International Scientific Agriculture Symposium: Agrosym 2020; 2020 Oct 8-9; Jahorina, Republika Srpska, Bosnia and Herzegovina (2020):152,
https://hdl.handle.net/21.15107/rcub_ibiss_5438 .

TY  - JOUR
AU  - Dragićević, Milan
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3756
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4966
AB  - Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.
PB  - Oxford University Press
T2  - Glycobiology
T1  - ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R
IS  - 1
IS  - 1
VL  - 30
VL  - 30
DO  - 10.1093/glycob/cwz072
SP  - 19
SP  - 19
EP  - 35
EP  - 35
ER  - 

@article{
author = "Dragićević, Milan and Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.",
publisher = "Oxford University Press",
journal = "Glycobiology",
title = "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R",
number = "1, 1",
volume = "30, 30",
doi = "10.1093/glycob/cwz072",
pages = "19-19-35-35"
}

Dragićević, M., Paunović, D., Bogdanović, M., Todorović, S.,& Simonović, A.. (2020). ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology
Oxford University Press., 30(1), 19-35.
https://doi.org/10.1093/glycob/cwz072

Dragićević M, Paunović D, Bogdanović M, Todorović S, Simonović A. ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology. 2020;30(1):19-35.
doi:10.1093/glycob/cwz072 .

Dragićević, Milan, Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R" in Glycobiology, 30, no. 1 (2020):19-35,
https://doi.org/10.1093/glycob/cwz072 . .

TY  - JOUR
AU  - Dragićević, Milan
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3756
AB  - Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.
PB  - Oxford University Press
T2  - Glycobiology
T1  - ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R
IS  - 1
IS  - 1
VL  - 30
VL  - 30
DO  - 10.1093/glycob/cwz072
SP  - 19
SP  - 19
EP  - 35
EP  - 35
ER  - 

@article{
author = "Dragićević, Milan and Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Hydroxyproline-rich glycoproteins (HRGPs) are one of the most complex families of macromolecules found in plants, due to the diversity of glycans decorating the protein backbone, as well as the heterogeneity of the protein backbones. While this diversity is responsible for a wide array of physiological functions associated with HRGPs, it hinders attempts for homology-based identification. Current approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences. Ragp is an R package for mining and analysis of HRGPs, with emphasis on arabinogalactan proteins. The ragp filtering pipeline exploits one of the HRGPs key features, the presence of hydroxyprolines which represent glycosylation sites. Main package features include prediction of proline hydroxylation sites, amino acid motif and bias analyses, efficient communication with web servers for prediction of N-terminal signal peptides, glycosylphosphatidylinositol modification sites and disordered regions and the ability to annotate sequences through hmmscan and subsequent GO enrichment, based on predicted Pfam domains. As such, ragp extends R’s rich ecosystem for high-throughput sequence data analyses. The ragp R package is available under the MIT Open Source license and is freely available to download from GitHub at: https://github.com/missuse/ragp.",
publisher = "Oxford University Press",
journal = "Glycobiology",
title = "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R",
number = "1, 1",
volume = "30, 30",
doi = "10.1093/glycob/cwz072",
pages = "19-19-35-35"
}

Dragićević, M., Paunović, D., Bogdanović, M., Todorović, S.,& Simonović, A.. (2020). ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology
Oxford University Press., 30(1), 19-35.
https://doi.org/10.1093/glycob/cwz072

Dragićević M, Paunović D, Bogdanović M, Todorović S, Simonović A. ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R. in Glycobiology. 2020;30(1):19-35.
doi:10.1093/glycob/cwz072 .

Dragićević, Milan, Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, "ragp: Pipeline for mining of plant hydroxyproline-rich glycoproteins with implementation in R" in Glycobiology, 30, no. 1 (2020):19-35,
https://doi.org/10.1093/glycob/cwz072 . .

TY  - JOUR
AU  - Stanojković, Jelena
AU  - Todorović, Slađana
AU  - Pećinar, Ilinka
AU  - Lević, Steva
AU  - Ćalić, Snežana
AU  - Janošević, Dušica
PY  - 2020
UR  - https://linkinghub.elsevier.com/retrieve/pii/S0926669020310189
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4071
AB  - Glandular trichomes are secretory organs that vary greatly in size, shape, location, type, and composition of secondary metabolites that are synthesized in them. They represent a protective chemical barrier and metabolic factories for the synthesis of bioactive compounds. We evaluated the effect of sucrose on the growth and biomass production, as well as on the distribution, density, and chemical composition of leaf glandular trichomes developed in vitro cultured Inula britannica, an important medical and aromatic species. Nodal segments (5 mm) were cultivated on the basal Murashige and Skoog medium with different concentrations (0 M, 0.01 M, 0.06 M, 0.1 M and 0.3 M) of sucrose. The lack of sugar does not retard growth, while a high sugar concentration inhibits biomass accumulation in vitro. The density and number of leaf glandular trichomes are changed with the medium composition variation. Morphoanatomical and histochemical analyses of the trichomes of the cultured I. britannica applying SEM, conventional light, fluorescent and Raman microscopy revealed the presence of non- glandular and biseriate glandular trichomes on the leaf surface. The histochemical analysis proved that glandular trichomes synthesized a complex mixture of biomolecules. The Raman microscopy analysis of glandular trichomes confirmed the presence of terpenes, most probably the bicyclic monoterpenes and sesquiterpenes. The multivariate analysis, based on PCA, was applied to distinguish among the glandular trichomes of three sugar concentrations: sugar-free medium (0 M), optimal (0.1 M) and the highest sucrose concentration (0.3 M). The main differences between the chemical profile of the leaf glandular trichomes of the plants grown on the 0 M and the chemical profile of the trichomes developed on the 0.1 and 0.3 M medium come mainly from phenolic compounds and to a smaller degree from cyclic terpenes, while the chemical profile of the glandular trichomes grown on the 0.1 M and 0.3 M differs considerably from the trichomes grown on the sugar-free medium in the polysaccharide cell wall ingredients. Most differences between the chemical profile of the glandular trichomes developed on 0 M and 0.3 M and the chemical profile of the trichomes grown on the 0.1 M of sucrose, come from phenolic compounds.
PB  - Elsevier BV
T2  - Industrial Crops and Products
T1  - Leaf glandular trichomes of micropropagated Inula britannica – Effect of sucrose on trichome density, distribution and chemical profile
DO  - 10.1016/j.indcrop.2020.113101
SP  - 113101
ER  - 

@article{
author = "Stanojković, Jelena and Todorović, Slađana and Pećinar, Ilinka and Lević, Steva and Ćalić, Snežana and Janošević, Dušica",
year = "2020",
abstract = "Glandular trichomes are secretory organs that vary greatly in size, shape, location, type, and composition of secondary metabolites that are synthesized in them. They represent a protective chemical barrier and metabolic factories for the synthesis of bioactive compounds. We evaluated the effect of sucrose on the growth and biomass production, as well as on the distribution, density, and chemical composition of leaf glandular trichomes developed in vitro cultured Inula britannica, an important medical and aromatic species. Nodal segments (5 mm) were cultivated on the basal Murashige and Skoog medium with different concentrations (0 M, 0.01 M, 0.06 M, 0.1 M and 0.3 M) of sucrose. The lack of sugar does not retard growth, while a high sugar concentration inhibits biomass accumulation in vitro. The density and number of leaf glandular trichomes are changed with the medium composition variation. Morphoanatomical and histochemical analyses of the trichomes of the cultured I. britannica applying SEM, conventional light, fluorescent and Raman microscopy revealed the presence of non- glandular and biseriate glandular trichomes on the leaf surface. The histochemical analysis proved that glandular trichomes synthesized a complex mixture of biomolecules. The Raman microscopy analysis of glandular trichomes confirmed the presence of terpenes, most probably the bicyclic monoterpenes and sesquiterpenes. The multivariate analysis, based on PCA, was applied to distinguish among the glandular trichomes of three sugar concentrations: sugar-free medium (0 M), optimal (0.1 M) and the highest sucrose concentration (0.3 M). The main differences between the chemical profile of the leaf glandular trichomes of the plants grown on the 0 M and the chemical profile of the trichomes developed on the 0.1 and 0.3 M medium come mainly from phenolic compounds and to a smaller degree from cyclic terpenes, while the chemical profile of the glandular trichomes grown on the 0.1 M and 0.3 M differs considerably from the trichomes grown on the sugar-free medium in the polysaccharide cell wall ingredients. Most differences between the chemical profile of the glandular trichomes developed on 0 M and 0.3 M and the chemical profile of the trichomes grown on the 0.1 M of sucrose, come from phenolic compounds.",
publisher = "Elsevier BV",
journal = "Industrial Crops and Products",
title = "Leaf glandular trichomes of micropropagated Inula britannica – Effect of sucrose on trichome density, distribution and chemical profile",
doi = "10.1016/j.indcrop.2020.113101",
pages = "113101"
}

Stanojković, J., Todorović, S., Pećinar, I., Lević, S., Ćalić, S.,& Janošević, D.. (2020). Leaf glandular trichomes of micropropagated Inula britannica – Effect of sucrose on trichome density, distribution and chemical profile. in Industrial Crops and Products
Elsevier BV., 113101.
https://doi.org/10.1016/j.indcrop.2020.113101

Stanojković J, Todorović S, Pećinar I, Lević S, Ćalić S, Janošević D. Leaf glandular trichomes of micropropagated Inula britannica – Effect of sucrose on trichome density, distribution and chemical profile. in Industrial Crops and Products. 2020;:113101.
doi:10.1016/j.indcrop.2020.113101 .

Stanojković, Jelena, Todorović, Slađana, Pećinar, Ilinka, Lević, Steva, Ćalić, Snežana, Janošević, Dušica, "Leaf glandular trichomes of micropropagated Inula britannica – Effect of sucrose on trichome density, distribution and chemical profile" in Industrial Crops and Products (2020):113101,
https://doi.org/10.1016/j.indcrop.2020.113101 . .

TY  - JOUR
AU  - Belić, Maja
AU  - Zdravković-Korać, Snežana
AU  - Janošević, Dušica
AU  - Savić, Jelena
AU  - Todorović, Slađana
AU  - Banjac, Nevena
AU  - Milojević, Jelena
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3774
AB  - Gibberellins (GAs) play a pivotal role in the induction of somatic embryogenesis from in vitro root apices of spinach plants. With the aim to understand the role of GAs in this process and to improve somatic embryo (SE) regeneration efficiency, the impact of light and GAs on SE initiation from the in vitro root apices was studied. The root sections were isolated from in vitro-grown SE-derived plants and placed on medium containing 20 µM α-naphthaleneacetic acid (NAA) and 0–10 µM GA3 or GA1, and cultivated under light conditions or in darkness. The most efficient SE regeneration response (100% regenerating SEs and 40.73 SEs per root apices) was achieved only in the presence of both light and GAs, with GA3 always exhibiting much stronger effect than GA1. Considering that light enhances GAs biosynthesis and the necessity of GAs for SE initiation, the expression levels of genes encoding the key enzymes involved in the final steps of GAs synthesis (SoGA20-ox1 and SoGA3-ox1) and deactivation (SoGA2-ox1, SoGA2-ox2 and SoGA2-ox3) were analyzed. Light enhanced the expression of all five GA-ox genes, while exogenously supplied NAA + GA3 provoked downregulation of SoGA20-ox1 and SoGA3-ox1 and upregulation of SoGA2ox-2 and SoGA2ox-3 expression. The expression of SoGA2ox-1 only slightly decreased. The results indicated the capability of isolated spinach roots to perceive the light and autonomously produce GAs. The expression levels of genes encoding key enzymes involved in GA biosynthesis suggest that lower levels of GAs favor SE initiation.
PB  - Springer
T2  - Plant Cell, Tissue and Organ Culture
T1  - Gibberellins and light synergistically promote somatic embryogenesis from the in vitro apical root sections of spinach
VL  - 142
DO  - 10.1007/s11240-020-01878-3
SP  - 537
EP  - 548
ER  - 

@article{
author = "Belić, Maja and Zdravković-Korać, Snežana and Janošević, Dušica and Savić, Jelena and Todorović, Slađana and Banjac, Nevena and Milojević, Jelena",
year = "2020",
abstract = "Gibberellins (GAs) play a pivotal role in the induction of somatic embryogenesis from in vitro root apices of spinach plants. With the aim to understand the role of GAs in this process and to improve somatic embryo (SE) regeneration efficiency, the impact of light and GAs on SE initiation from the in vitro root apices was studied. The root sections were isolated from in vitro-grown SE-derived plants and placed on medium containing 20 µM α-naphthaleneacetic acid (NAA) and 0–10 µM GA3 or GA1, and cultivated under light conditions or in darkness. The most efficient SE regeneration response (100% regenerating SEs and 40.73 SEs per root apices) was achieved only in the presence of both light and GAs, with GA3 always exhibiting much stronger effect than GA1. Considering that light enhances GAs biosynthesis and the necessity of GAs for SE initiation, the expression levels of genes encoding the key enzymes involved in the final steps of GAs synthesis (SoGA20-ox1 and SoGA3-ox1) and deactivation (SoGA2-ox1, SoGA2-ox2 and SoGA2-ox3) were analyzed. Light enhanced the expression of all five GA-ox genes, while exogenously supplied NAA + GA3 provoked downregulation of SoGA20-ox1 and SoGA3-ox1 and upregulation of SoGA2ox-2 and SoGA2ox-3 expression. The expression of SoGA2ox-1 only slightly decreased. The results indicated the capability of isolated spinach roots to perceive the light and autonomously produce GAs. The expression levels of genes encoding key enzymes involved in GA biosynthesis suggest that lower levels of GAs favor SE initiation.",
publisher = "Springer",
journal = "Plant Cell, Tissue and Organ Culture",
title = "Gibberellins and light synergistically promote somatic embryogenesis from the in vitro apical root sections of spinach",
volume = "142",
doi = "10.1007/s11240-020-01878-3",
pages = "537-548"
}

Belić, M., Zdravković-Korać, S., Janošević, D., Savić, J., Todorović, S., Banjac, N.,& Milojević, J.. (2020). Gibberellins and light synergistically promote somatic embryogenesis from the in vitro apical root sections of spinach. in Plant Cell, Tissue and Organ Culture
Springer., 142, 537-548.
https://doi.org/10.1007/s11240-020-01878-3

Belić M, Zdravković-Korać S, Janošević D, Savić J, Todorović S, Banjac N, Milojević J. Gibberellins and light synergistically promote somatic embryogenesis from the in vitro apical root sections of spinach. in Plant Cell, Tissue and Organ Culture. 2020;142:537-548.
doi:10.1007/s11240-020-01878-3 .

Belić, Maja, Zdravković-Korać, Snežana, Janošević, Dušica, Savić, Jelena, Todorović, Slađana, Banjac, Nevena, Milojević, Jelena, "Gibberellins and light synergistically promote somatic embryogenesis from the in vitro apical root sections of spinach" in Plant Cell, Tissue and Organ Culture, 142 (2020):537-548,
https://doi.org/10.1007/s11240-020-01878-3 . .

TY  - JOUR
AU  - Bogdanović, Milica
AU  - Cankar, Katarina
AU  - Dragićević, Milan
AU  - Bouwmeester, Harro
AU  - Beekwilder, Jules
AU  - Simonović, Ana
AU  - Todorović, Slađana
PY  - 2020
UR  - https://www.tandfonline.com/doi/full/10.1080/21645698.2019.1681868
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3520
AB  - Chicory (Cichorium intybus L.) is a medicinal and industrial plant from the Asteraceae family that produces a variety of sesquiterpene lactones (STLs), most importantly bitter guaianolides: lactucin, lactucopicrin and 8-deoxylactucin as well as their modified forms such as oxalates. These compounds have medicinal properties; however, they also hamper the extraction of inulin - a very important food industry product from chicory roots. The first step in guaianolide biosynthesis is catalyzed by germacrene A synthase (GAS) which in chicory exists in two isoforms - GAS long (encoded by CiGASlo) and GAS short (encoded by CiGASsh). AmiRNA silencing was used to obtain plants with reduced GAS gene expression and level of downstream metabolites, guaianolide-15-oxalates, as the major STLs in chicory. This approach could be beneficial for engineering new chicory varieties with varying STL content, and especially varieties with reduced bitter compounds more suitable for inulin production.
T2  - GM Crops & Food
T1  - Silencing of germacrene A synthase genes reduces guaianolide oxalate content in Cichorium intybus L.
IS  - 1
VL  - 11
DO  - 10.1080/21645698.2019.1681868
SP  - 54
EP  - 66
ER  - 

@article{
author = "Bogdanović, Milica and Cankar, Katarina and Dragićević, Milan and Bouwmeester, Harro and Beekwilder, Jules and Simonović, Ana and Todorović, Slađana",
year = "2020",
abstract = "Chicory (Cichorium intybus L.) is a medicinal and industrial plant from the Asteraceae family that produces a variety of sesquiterpene lactones (STLs), most importantly bitter guaianolides: lactucin, lactucopicrin and 8-deoxylactucin as well as their modified forms such as oxalates. These compounds have medicinal properties; however, they also hamper the extraction of inulin - a very important food industry product from chicory roots. The first step in guaianolide biosynthesis is catalyzed by germacrene A synthase (GAS) which in chicory exists in two isoforms - GAS long (encoded by CiGASlo) and GAS short (encoded by CiGASsh). AmiRNA silencing was used to obtain plants with reduced GAS gene expression and level of downstream metabolites, guaianolide-15-oxalates, as the major STLs in chicory. This approach could be beneficial for engineering new chicory varieties with varying STL content, and especially varieties with reduced bitter compounds more suitable for inulin production.",
journal = "GM Crops & Food",
title = "Silencing of germacrene A synthase genes reduces guaianolide oxalate content in Cichorium intybus L.",
number = "1",
volume = "11",
doi = "10.1080/21645698.2019.1681868",
pages = "54-66"
}

Bogdanović, M., Cankar, K., Dragićević, M., Bouwmeester, H., Beekwilder, J., Simonović, A.,& Todorović, S.. (2020). Silencing of germacrene A synthase genes reduces guaianolide oxalate content in Cichorium intybus L.. in GM Crops & Food, 11(1), 54-66.
https://doi.org/10.1080/21645698.2019.1681868

Bogdanović M, Cankar K, Dragićević M, Bouwmeester H, Beekwilder J, Simonović A, Todorović S. Silencing of germacrene A synthase genes reduces guaianolide oxalate content in Cichorium intybus L.. in GM Crops & Food. 2020;11(1):54-66.
doi:10.1080/21645698.2019.1681868 .

Bogdanović, Milica, Cankar, Katarina, Dragićević, Milan, Bouwmeester, Harro, Beekwilder, Jules, Simonović, Ana, Todorović, Slađana, "Silencing of germacrene A synthase genes reduces guaianolide oxalate content in Cichorium intybus L." in GM Crops & Food, 11, no. 1 (2020):54-66,
https://doi.org/10.1080/21645698.2019.1681868 . .

TY  - JOUR
AU  - Cvetković, Stefana
AU  - Todorović, Slađana
AU  - Nastasijević, Branislav
AU  - Mitić-Ćulafić, Dragana
AU  - Đukanović, Stefana
AU  - Knežević-Vukčević, Jelena
AU  - Nikolić, Biljana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3712
AB  - Medicinal plant Gentiana lutea is considered as an official drug for gastrointestinal disorders in many pharmacopoeias. Its uncontrolled overexploitation led to the protection regime and encouraged development of in vitro culture. The aim of this work was to chemically characterize root and leaf methanol extracts of plant grown in plantation and in vitro conditions, and to determine their antigenotoxicity against heterocyclic aromatic amines IQ and PhIP, the food-borne mutagens that are formed during high temperature cooking of protein-reach foods. High yields and growth ratios were determined for in vitro plants. Higher content of polyphenols and flavonoids were determined in aerial parts, while UPLC-MS/MS analysis pointed at the richness of in vitro grown shoot extract (GLvS) in active constituents, and high amounts of gentiopicroside in all tested extracts. Notable amounts of sweroside were detected in plantation root extract (GLR) and in GLvS, and of loganic acid in plantation leaf extract (GLL) and GLvS. Two experimental models for genotoxicity/antigenotoxicity study, i.e. SOS/umuC test with metabolic activation (addition of rat liver S9 fraction) and alkaline comet assay on hepatocellur carcinoma HepG2 cells indicated dual effects: genotoxic of high and antigenotoxic of lower non-genotoxic doses. While in vitro extracts were genotoxic in both models, plantation extracts were active only in SOS/umuC with S9. In contrast, inhibition of genotoxicity was observed in both models for all extracts (up to 83 %). Results of DPPH assay indicated that antioxidativity could be responsible for antigenotoxic properties. In conclusion, genoprotective effect encourages further investigation of antigenotoxicity, while high growth ratio and richness of GLvS in active compounds justify the use of in vitro cultivation method.
PB  - Elsevier B.V.
T2  - Industrial Crops and Products
T1  - Assessment of genoprotective effects of Gentiana lutea extracts prepared from plants grown in field and in vitro
VL  - 154
DO  - 10.1016/j.indcrop.2020.112690
SP  - 112690
ER  - 

@article{
author = "Cvetković, Stefana and Todorović, Slađana and Nastasijević, Branislav and Mitić-Ćulafić, Dragana and Đukanović, Stefana and Knežević-Vukčević, Jelena and Nikolić, Biljana",
year = "2020",
abstract = "Medicinal plant Gentiana lutea is considered as an official drug for gastrointestinal disorders in many pharmacopoeias. Its uncontrolled overexploitation led to the protection regime and encouraged development of in vitro culture. The aim of this work was to chemically characterize root and leaf methanol extracts of plant grown in plantation and in vitro conditions, and to determine their antigenotoxicity against heterocyclic aromatic amines IQ and PhIP, the food-borne mutagens that are formed during high temperature cooking of protein-reach foods. High yields and growth ratios were determined for in vitro plants. Higher content of polyphenols and flavonoids were determined in aerial parts, while UPLC-MS/MS analysis pointed at the richness of in vitro grown shoot extract (GLvS) in active constituents, and high amounts of gentiopicroside in all tested extracts. Notable amounts of sweroside were detected in plantation root extract (GLR) and in GLvS, and of loganic acid in plantation leaf extract (GLL) and GLvS. Two experimental models for genotoxicity/antigenotoxicity study, i.e. SOS/umuC test with metabolic activation (addition of rat liver S9 fraction) and alkaline comet assay on hepatocellur carcinoma HepG2 cells indicated dual effects: genotoxic of high and antigenotoxic of lower non-genotoxic doses. While in vitro extracts were genotoxic in both models, plantation extracts were active only in SOS/umuC with S9. In contrast, inhibition of genotoxicity was observed in both models for all extracts (up to 83 %). Results of DPPH assay indicated that antioxidativity could be responsible for antigenotoxic properties. In conclusion, genoprotective effect encourages further investigation of antigenotoxicity, while high growth ratio and richness of GLvS in active compounds justify the use of in vitro cultivation method.",
publisher = "Elsevier B.V.",
journal = "Industrial Crops and Products",
title = "Assessment of genoprotective effects of Gentiana lutea extracts prepared from plants grown in field and in vitro",
volume = "154",
doi = "10.1016/j.indcrop.2020.112690",
pages = "112690"
}

Cvetković, S., Todorović, S., Nastasijević, B., Mitić-Ćulafić, D., Đukanović, S., Knežević-Vukčević, J.,& Nikolić, B.. (2020). Assessment of genoprotective effects of Gentiana lutea extracts prepared from plants grown in field and in vitro. in Industrial Crops and Products
Elsevier B.V.., 154, 112690.
https://doi.org/10.1016/j.indcrop.2020.112690

Cvetković S, Todorović S, Nastasijević B, Mitić-Ćulafić D, Đukanović S, Knežević-Vukčević J, Nikolić B. Assessment of genoprotective effects of Gentiana lutea extracts prepared from plants grown in field and in vitro. in Industrial Crops and Products. 2020;154:112690.
doi:10.1016/j.indcrop.2020.112690 .

Cvetković, Stefana, Todorović, Slađana, Nastasijević, Branislav, Mitić-Ćulafić, Dragana, Đukanović, Stefana, Knežević-Vukčević, Jelena, Nikolić, Biljana, "Assessment of genoprotective effects of Gentiana lutea extracts prepared from plants grown in field and in vitro" in Industrial Crops and Products, 154 (2020):112690,
https://doi.org/10.1016/j.indcrop.2020.112690 . .

TY  - JOUR
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Bogdanović, Milica
AU  - Paunović, Danijela
AU  - Giurato, Giorgio
AU  - Filipović, Biljana
AU  - Subotić, Angelina
AU  - Todorović, Slađana
AU  - Simonović, Ana
PY  - 2020
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3686
AB  - Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.
PB  - Springer
T2  - Plant Cell, Tissue and Organ Culture
T1  - Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis
IS  - 2
VL  - 141
DO  - 10.1007/s11240-020-01801-w
SP  - 417
EP  - 433
ER  - 

@article{
author = "Ćuković, Katarina and Dragićević, Milan and Bogdanović, Milica and Paunović, Danijela and Giurato, Giorgio and Filipović, Biljana and Subotić, Angelina and Todorović, Slađana and Simonović, Ana",
year = "2020",
abstract = "Centaurium erythraea Rafn. (common centaury, Gentianaceae) is a medicinal plant with great regeneration potential and developmental plasticity in vitro. Centaury can be regenerated from leaf explants by both somatic embryogenesis (SE) and shoot development (SD). We believe that its regeneration potential and developmental plasticity rest on high activity of certain genes, which may not be active or present in species recalcitrant to in vitro regeneration. However, there are no sequenced Gentianaceae genomes to support investigation of the molecular events during SE or SD. To this end, we have sequenced six centaury transcriptomes (embryogenic calli, globular somatic embryos, cotyledonary somatic embryos, adventitious buds, leaves and roots of in vitro grown plants) and de novo assembled centaury referent transcriptome comprising 105.726 genes. The high quality and completeness transcriptome was functionally annotated against NCBI nt, Swissprot and PFAM databases with KOG and GO enrichment. In addition, 11 housekeeping and functional genes were validated for expression stability in 27 tissue samples representing the processes of SE and SD, plants from nature and wounded tissues using GeNorm and NormFinder. The most stable genes that can be used for expression studies during SE, SD and in vitro manipulations are Ribosomal protein L2 (RPL2) and TATA binding protein 1 (TBP1) in combination with RAS (Rat Sarcoma)-related Nuclear protein (RAN) or Adenosine kinase (AK). These results comprise a complete framework for the search for genes involved in SE and SD, but may also be useful in identifying genes involved in biosynthesis of C. erythraea secondary metabolites.",
publisher = "Springer",
journal = "Plant Cell, Tissue and Organ Culture",
title = "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis",
number = "2",
volume = "141",
doi = "10.1007/s11240-020-01801-w",
pages = "417-433"
}

Ćuković, K., Dragićević, M., Bogdanović, M., Paunović, D., Giurato, G., Filipović, B., Subotić, A., Todorović, S.,& Simonović, A.. (2020). Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture
Springer., 141(2), 417-433.
https://doi.org/10.1007/s11240-020-01801-w

Ćuković K, Dragićević M, Bogdanović M, Paunović D, Giurato G, Filipović B, Subotić A, Todorović S, Simonović A. Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis. in Plant Cell, Tissue and Organ Culture. 2020;141(2):417-433.
doi:10.1007/s11240-020-01801-w .

Ćuković, Katarina, Dragićević, Milan, Bogdanović, Milica, Paunović, Danijela, Giurato, Giorgio, Filipović, Biljana, Subotić, Angelina, Todorović, Slađana, Simonović, Ana, "Plant regeneration in leaf culture of Centaurium erythraea Rafn. Part 3: de novo transcriptome assembly and validation of housekeeping genes for studies of in vitro morphogenesis" in Plant Cell, Tissue and Organ Culture, 141, no. 2 (2020):417-433,
https://doi.org/10.1007/s11240-020-01801-w . .

TY  - CONF
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Todorović, Slađana
AU  - Bogdanović, Milica
AU  - Simonović, Ana
PY  - 2019
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5439
AB  - Centaurium erythraea Rafn. (Gentianaceae) represents a well-known medicinal plant rich in secondary metabolites and an appropriate model system for studying developmental biology due to its great developmental plasticity in vitro. One of the most unique manifestations of this characteristic in plants is somatic embryogenesis (SE), the development of embryos from somatic cells. SE initiation and progressing of the embryo through different developmental stages involves gene reprogramming and differential expression of numerous genes. Our current research focuses on characterizing novel SE-related genes in centaury tissues using next-generation RNA sequencing data and quantitative real-time PCR (qPCR). Six different centaury tissues, including embryogenic calli, globular and cotiledonary somatic embryos were subjected to ultra-high-throughput sequencing on an Illumina HiSeq 2500 platform, followed by de novo transcriptome assembly. FPKM (fragments per kilobase of exon model per million reads mapped) was used to evaluate in silico expression of functionally annotated transcripts. The generated transcriptome data were subsequently used for discovering genes with potential roles in centaury SE. Potential SE markers were excavated focusing on transcripts with greater than eight fold change in FPKM values in embryogenic tissues compared to non-embryogenic ones. Based on these criteria, twenty transcripts were chosen,
four with completely unknown function. Expression analysis of selected genes was carried out by qPCR using specific primers in different embryogenic and non-embryogenic centaury tissues. Identified genes with differential expression during SE will be further characterized by overexpression and silencing in centaury.
PB  - East Sarajevo: Faculty of Agriculture
C3  - Book of abstracts: X International Scientific Agriculture Symposium: Agrosym 2019; 2019 Oct 3-6; Jahorina, Republika Srpska, Bosnia and Herzegovina
T1  - Selection of differentially expressed genes in Centaurium erythraea Rafn. during in vitro somatic embryogenesis
SP  - 226
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5439
ER  - 

@conference{
author = "Ćuković, Katarina and Dragićević, Milan and Todorović, Slađana and Bogdanović, Milica and Simonović, Ana",
year = "2019",
abstract = "Centaurium erythraea Rafn. (Gentianaceae) represents a well-known medicinal plant rich in secondary metabolites and an appropriate model system for studying developmental biology due to its great developmental plasticity in vitro. One of the most unique manifestations of this characteristic in plants is somatic embryogenesis (SE), the development of embryos from somatic cells. SE initiation and progressing of the embryo through different developmental stages involves gene reprogramming and differential expression of numerous genes. Our current research focuses on characterizing novel SE-related genes in centaury tissues using next-generation RNA sequencing data and quantitative real-time PCR (qPCR). Six different centaury tissues, including embryogenic calli, globular and cotiledonary somatic embryos were subjected to ultra-high-throughput sequencing on an Illumina HiSeq 2500 platform, followed by de novo transcriptome assembly. FPKM (fragments per kilobase of exon model per million reads mapped) was used to evaluate in silico expression of functionally annotated transcripts. The generated transcriptome data were subsequently used for discovering genes with potential roles in centaury SE. Potential SE markers were excavated focusing on transcripts with greater than eight fold change in FPKM values in embryogenic tissues compared to non-embryogenic ones. Based on these criteria, twenty transcripts were chosen,
four with completely unknown function. Expression analysis of selected genes was carried out by qPCR using specific primers in different embryogenic and non-embryogenic centaury tissues. Identified genes with differential expression during SE will be further characterized by overexpression and silencing in centaury.",
publisher = "East Sarajevo: Faculty of Agriculture",
journal = "Book of abstracts: X International Scientific Agriculture Symposium: Agrosym 2019; 2019 Oct 3-6; Jahorina, Republika Srpska, Bosnia and Herzegovina",
title = "Selection of differentially expressed genes in Centaurium erythraea Rafn. during in vitro somatic embryogenesis",
pages = "226",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5439"
}

Ćuković, K., Dragićević, M., Todorović, S., Bogdanović, M.,& Simonović, A.. (2019). Selection of differentially expressed genes in Centaurium erythraea Rafn. during in vitro somatic embryogenesis. in Book of abstracts: X International Scientific Agriculture Symposium: Agrosym 2019; 2019 Oct 3-6; Jahorina, Republika Srpska, Bosnia and Herzegovina
East Sarajevo: Faculty of Agriculture., 226.
https://hdl.handle.net/21.15107/rcub_ibiss_5439

Ćuković K, Dragićević M, Todorović S, Bogdanović M, Simonović A. Selection of differentially expressed genes in Centaurium erythraea Rafn. during in vitro somatic embryogenesis. in Book of abstracts: X International Scientific Agriculture Symposium: Agrosym 2019; 2019 Oct 3-6; Jahorina, Republika Srpska, Bosnia and Herzegovina. 2019;:226.
https://hdl.handle.net/21.15107/rcub_ibiss_5439 .

Ćuković, Katarina, Dragićević, Milan, Todorović, Slađana, Bogdanović, Milica, Simonović, Ana, "Selection of differentially expressed genes in Centaurium erythraea Rafn. during in vitro somatic embryogenesis" in Book of abstracts: X International Scientific Agriculture Symposium: Agrosym 2019; 2019 Oct 3-6; Jahorina, Republika Srpska, Bosnia and Herzegovina (2019):226,
https://hdl.handle.net/21.15107/rcub_ibiss_5439 .

TY  - JOUR
AU  - Dragićević, Milan
AU  - Ćuković, Katarina
AU  - Zdravković-Korać, Snežana
AU  - Simonović, Ana
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
PY  - 2019
UR  - http://www.doiserbia.nb.rs/Article.aspx?ID=0354-46641900026D
UR  - http://www.serbiosoc.org.rs/arch/index.php/abs/article/view/4099
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3568
AB  - Glutamine synthetase (E.C. 6.3.1.2) is a key enzyme of plant nitrogen metabolism that assimilates ammonia into glutamine. The Arabidopsis thaliana genome encodes one chloroplastic (GLN2) and five cytosolic (GLN1;1 – GLN1;5) isoforms with different expression patterns, kinetic properties, regulation and functions. Physiological roles of different isoforms have been elucidated mainly by studying knockout mutants. However, the role of GLN1;5, which is expressed in dry seeds, remains unknown. To clarifty the function of GLN1;5, we studied a GLN1;5 knockout line (GLN1;5KO) homozygous for T-DNA insertion within the GLN1;5. GLN1;5 deficiency results in a phenotype with slightly delayed bolting and fewer siliques. The dry weight of GLN1;5KO seeds was 73.3% of wild-type (WT) seed weight, with seed length 90.9% of WT seeds. Finally, only 18.33% of the mutant seeds germinated in water within 10 days in comparison to 34.67% of WT seeds. KNO3 strongly stimulated germination of both GLN1;5KO and WT seeds, while germination in the presence of increasing NH4Cl concentrations potentiated the differences between the two genotypes. It can be concluded that GLN1;5 activity supports silique development and grain filling and that it has a role in ammonium reassimilation in the seed, as well as assimilation and/or detoxification of ammonium from the environment.
T2  - Archives of Biological Sciences
T1  - Elucidation of the role of glutamine synthetase seed isoform GLN1;5 in Arabidopsis thaliana (L.) with a reverse genetics approach
IS  - 3
VL  - 71
DO  - 10.2298/ABS190315026D
SP  - 443
EP  - 453
ER  - 

@article{
author = "Dragićević, Milan and Ćuković, Katarina and Zdravković-Korać, Snežana and Simonović, Ana and Bogdanović, Milica and Todorović, Slađana",
year = "2019",
abstract = "Glutamine synthetase (E.C. 6.3.1.2) is a key enzyme of plant nitrogen metabolism that assimilates ammonia into glutamine. The Arabidopsis thaliana genome encodes one chloroplastic (GLN2) and five cytosolic (GLN1;1 – GLN1;5) isoforms with different expression patterns, kinetic properties, regulation and functions. Physiological roles of different isoforms have been elucidated mainly by studying knockout mutants. However, the role of GLN1;5, which is expressed in dry seeds, remains unknown. To clarifty the function of GLN1;5, we studied a GLN1;5 knockout line (GLN1;5KO) homozygous for T-DNA insertion within the GLN1;5. GLN1;5 deficiency results in a phenotype with slightly delayed bolting and fewer siliques. The dry weight of GLN1;5KO seeds was 73.3% of wild-type (WT) seed weight, with seed length 90.9% of WT seeds. Finally, only 18.33% of the mutant seeds germinated in water within 10 days in comparison to 34.67% of WT seeds. KNO3 strongly stimulated germination of both GLN1;5KO and WT seeds, while germination in the presence of increasing NH4Cl concentrations potentiated the differences between the two genotypes. It can be concluded that GLN1;5 activity supports silique development and grain filling and that it has a role in ammonium reassimilation in the seed, as well as assimilation and/or detoxification of ammonium from the environment.",
journal = "Archives of Biological Sciences",
title = "Elucidation of the role of glutamine synthetase seed isoform GLN1;5 in Arabidopsis thaliana (L.) with a reverse genetics approach",
number = "3",
volume = "71",
doi = "10.2298/ABS190315026D",
pages = "443-453"
}

Dragićević, M., Ćuković, K., Zdravković-Korać, S., Simonović, A., Bogdanović, M.,& Todorović, S.. (2019). Elucidation of the role of glutamine synthetase seed isoform GLN1;5 in Arabidopsis thaliana (L.) with a reverse genetics approach. in Archives of Biological Sciences, 71(3), 443-453.
https://doi.org/10.2298/ABS190315026D

Dragićević M, Ćuković K, Zdravković-Korać S, Simonović A, Bogdanović M, Todorović S. Elucidation of the role of glutamine synthetase seed isoform GLN1;5 in Arabidopsis thaliana (L.) with a reverse genetics approach. in Archives of Biological Sciences. 2019;71(3):443-453.
doi:10.2298/ABS190315026D .

Dragićević, Milan, Ćuković, Katarina, Zdravković-Korać, Snežana, Simonović, Ana, Bogdanović, Milica, Todorović, Slađana, "Elucidation of the role of glutamine synthetase seed isoform GLN1;5 in Arabidopsis thaliana (L.) with a reverse genetics approach" in Archives of Biological Sciences, 71, no. 3 (2019):443-453,
https://doi.org/10.2298/ABS190315026D . .

TY  - JOUR
AU  - Bogdanović, Milica
AU  - Cankar, Katarina
AU  - Todorović, Slađana
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - van Houwelingen, Adele
AU  - Schijlen, Elio
AU  - Schipper, Bert
AU  - Gagneul, David
AU  - Hendriks, Theo
AU  - Quillet, Marie-Christine
AU  - Bouwmeester, Harro
AU  - Bosch, Dirk
AU  - Beekwilder, Jules
PY  - 2019
UR  - https://www.sciencedirect.com/science/article/pii/S092666901831063X?via%3Dihub
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/3212
AB  - Chicory (Cichorium intybus L.) produces bitter sesquiterpene lactones (STLs). Some enzymes in the biosynthetic pathway towards these compounds have been characterized. However, the genomic organization and tissue specificity of their biosynthesis is largely unknown. Concentrations of two sesquiterpene lactones and expression of genes involved in the first dedicated biosynthetic step were measured in different chicory tissues. BAC clones containing different genes encoding germacrene A synthase were sequenced, and revealed several tightly linked paralogs. Promoters of genes encoding two germacrene A synthases were fused to GFP and expressed in plants regenerated from transformed chicory hairy root cultures. Highest expression was observed in the epidermis of leaves and external root tissue. This work opens the possibility to select for chicory germplasm diversified in STL content, and to study their role in chicory in defence and physiology.
T2  - Industrial Crops and Products
T1  - Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae)
VL  - 129
DO  - 10.1016/J.INDCROP.2018.12.011
SP  - 253
EP  - 260
ER  - 

@article{
author = "Bogdanović, Milica and Cankar, Katarina and Todorović, Slađana and Dragićević, Milan and Simonović, Ana and van Houwelingen, Adele and Schijlen, Elio and Schipper, Bert and Gagneul, David and Hendriks, Theo and Quillet, Marie-Christine and Bouwmeester, Harro and Bosch, Dirk and Beekwilder, Jules",
year = "2019",
abstract = "Chicory (Cichorium intybus L.) produces bitter sesquiterpene lactones (STLs). Some enzymes in the biosynthetic pathway towards these compounds have been characterized. However, the genomic organization and tissue specificity of their biosynthesis is largely unknown. Concentrations of two sesquiterpene lactones and expression of genes involved in the first dedicated biosynthetic step were measured in different chicory tissues. BAC clones containing different genes encoding germacrene A synthase were sequenced, and revealed several tightly linked paralogs. Promoters of genes encoding two germacrene A synthases were fused to GFP and expressed in plants regenerated from transformed chicory hairy root cultures. Highest expression was observed in the epidermis of leaves and external root tissue. This work opens the possibility to select for chicory germplasm diversified in STL content, and to study their role in chicory in defence and physiology.",
journal = "Industrial Crops and Products",
title = "Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae)",
volume = "129",
doi = "10.1016/J.INDCROP.2018.12.011",
pages = "253-260"
}

Bogdanović, M., Cankar, K., Todorović, S., Dragićević, M., Simonović, A., van Houwelingen, A., Schijlen, E., Schipper, B., Gagneul, D., Hendriks, T., Quillet, M., Bouwmeester, H., Bosch, D.,& Beekwilder, J.. (2019). Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae). in Industrial Crops and Products, 129, 253-260.
https://doi.org/10.1016/J.INDCROP.2018.12.011

Bogdanović M, Cankar K, Todorović S, Dragićević M, Simonović A, van Houwelingen A, Schijlen E, Schipper B, Gagneul D, Hendriks T, Quillet M, Bouwmeester H, Bosch D, Beekwilder J. Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae). in Industrial Crops and Products. 2019;129:253-260.
doi:10.1016/J.INDCROP.2018.12.011 .

Bogdanović, Milica, Cankar, Katarina, Todorović, Slađana, Dragićević, Milan, Simonović, Ana, van Houwelingen, Adele, Schijlen, Elio, Schipper, Bert, Gagneul, David, Hendriks, Theo, Quillet, Marie-Christine, Bouwmeester, Harro, Bosch, Dirk, Beekwilder, Jules, "Tissue specific expression and genomic organization of bitter sesquiterpene lactone biosynthesis in Cichorium intybus L. (Asteraceae)" in Industrial Crops and Products, 129 (2019):253-260,
https://doi.org/10.1016/J.INDCROP.2018.12.011 . .

TY  - CONF
AU  - Bogdanović, Milica
AU  - Ćuković, Katarina
AU  - Dragićević, Milan
AU  - Simonović, Ana
AU  - Todorović, Slađana
PY  - 2018
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/5440
AB  - Organogenesis and somatic embryogenesis (SE) are often used for mass propagation
of high quality material of medicinal, endangered and rare plant species. In Centaurium
erythraea Rafn. (Gentianaceae), used as a model system in developmental studies, both
pathways can be exploited. SE from centaury leaf tissues starts with the formation of
embryogenic callus which develops into somatic embryos following globular, heart, torpedo and cotiledonary embryo phases. SE potential of leaf explants and embryogenic calli is highly dependent on concentration and ratio of added plant growth regulators, genotype, explant type and number of subcultures. Frequent (weekly) subculturing of the calli slows down growth and differentiation, whereas biweekly subculturing results in better embryogenic response. Higher CPPU to 2,4-D ratio drives the callus development towards embryo differentiation. Embryogenic potential of the callus cultures also depends on the presence of already formed globular embryos, since their removal reduces both growth and embryogenic potential. Once this potential is reduced, it cannot be restored by increasing exogenous hormone concentration. In order to further characterize and improve these processes in centaury, a documentation system was developed, using LED white light epi illumination, coupled with a smartphone camera with macro lens. Developmental processes were observed sequentially on leaf sections subjected to different 2,4-D and CPPU concentrations. Image processing of focal
stacks from developing explants was automated in Adobe Photoshop and Bridge. A relational database containing all relevant sample information and photographs was then built using Excel and R.
PB  - East Sarajevo: Faculty of Agriculture
C3  - Book of abstracts: IX International Scientific Agriculture Symposium: Agrosym 2018; 2018 Oct 4-7; Jahorina, Republika Srpska, Bosnia and Herzegovina
T1  - Somatic embryogenesis of Centaurium erythraea Rafn. time-lapse documentation of in vitro development
SP  - 347
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_5440
ER  - 

@conference{
author = "Bogdanović, Milica and Ćuković, Katarina and Dragićević, Milan and Simonović, Ana and Todorović, Slađana",
year = "2018",
abstract = "Organogenesis and somatic embryogenesis (SE) are often used for mass propagation
of high quality material of medicinal, endangered and rare plant species. In Centaurium
erythraea Rafn. (Gentianaceae), used as a model system in developmental studies, both
pathways can be exploited. SE from centaury leaf tissues starts with the formation of
embryogenic callus which develops into somatic embryos following globular, heart, torpedo and cotiledonary embryo phases. SE potential of leaf explants and embryogenic calli is highly dependent on concentration and ratio of added plant growth regulators, genotype, explant type and number of subcultures. Frequent (weekly) subculturing of the calli slows down growth and differentiation, whereas biweekly subculturing results in better embryogenic response. Higher CPPU to 2,4-D ratio drives the callus development towards embryo differentiation. Embryogenic potential of the callus cultures also depends on the presence of already formed globular embryos, since their removal reduces both growth and embryogenic potential. Once this potential is reduced, it cannot be restored by increasing exogenous hormone concentration. In order to further characterize and improve these processes in centaury, a documentation system was developed, using LED white light epi illumination, coupled with a smartphone camera with macro lens. Developmental processes were observed sequentially on leaf sections subjected to different 2,4-D and CPPU concentrations. Image processing of focal
stacks from developing explants was automated in Adobe Photoshop and Bridge. A relational database containing all relevant sample information and photographs was then built using Excel and R.",
publisher = "East Sarajevo: Faculty of Agriculture",
journal = "Book of abstracts: IX International Scientific Agriculture Symposium: Agrosym 2018; 2018 Oct 4-7; Jahorina, Republika Srpska, Bosnia and Herzegovina",
title = "Somatic embryogenesis of Centaurium erythraea Rafn. time-lapse documentation of in vitro development",
pages = "347",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_5440"
}

Bogdanović, M., Ćuković, K., Dragićević, M., Simonović, A.,& Todorović, S.. (2018). Somatic embryogenesis of Centaurium erythraea Rafn. time-lapse documentation of in vitro development. in Book of abstracts: IX International Scientific Agriculture Symposium: Agrosym 2018; 2018 Oct 4-7; Jahorina, Republika Srpska, Bosnia and Herzegovina
East Sarajevo: Faculty of Agriculture., 347.
https://hdl.handle.net/21.15107/rcub_ibiss_5440

Bogdanović M, Ćuković K, Dragićević M, Simonović A, Todorović S. Somatic embryogenesis of Centaurium erythraea Rafn. time-lapse documentation of in vitro development. in Book of abstracts: IX International Scientific Agriculture Symposium: Agrosym 2018; 2018 Oct 4-7; Jahorina, Republika Srpska, Bosnia and Herzegovina. 2018;:347.
https://hdl.handle.net/21.15107/rcub_ibiss_5440 .

Bogdanović, Milica, Ćuković, Katarina, Dragićević, Milan, Simonović, Ana, Todorović, Slađana, "Somatic embryogenesis of Centaurium erythraea Rafn. time-lapse documentation of in vitro development" in Book of abstracts: IX International Scientific Agriculture Symposium: Agrosym 2018; 2018 Oct 4-7; Jahorina, Republika Srpska, Bosnia and Herzegovina (2018):347,
https://hdl.handle.net/21.15107/rcub_ibiss_5440 .

TY  - CONF
AU  - Paunović, Danijela
AU  - Bogdanović, Milica
AU  - Todorović, Slađana
AU  - Simonović, Ana
AU  - Dragićević, Milan
PY  - 2018
UR  - https://ojs.pmf.uns.ac.rs/index.php/dbe_serbica/issue/view/25
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4341
AB  - Plant Hydroxyproline rich glycoproteins (HGRPs) comprise a highly diverse family of cell wall macromolecules, involved in a wide array of physiological functions such as cell expansion, somatic embryogenesis, self-incompatibility, signaling and pathogen responses. Due to biased amino acid composition, abundant in disorder promoting residues, HRGPs are intrinsically disordered proteins. The lack of a stable structure lessens the sequence constraints imposed on these proteins and hampers efforts for homology based identification. Current mining approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences.

Herby we present ragp, an R package for HGRP mining with a pipeline which emphasizes finding chimeric and short HRGP’s which is especially useful for identification of arabinogalactan proteins. The ragp pipeline exploits one of HGRP key features, the presence of hydroxyprolines which represent glycosylation sites. These sites are identified using a gradient boosting model trained on plant sequences with experimentally determined hydroxyprolines, based on the local (21-mer) sequence around the target prolines. The model was validated on a set of sequences which were not used during the model building, as well as by using several resampling approaches. Apart from prediction of proline hydroxylation main ragp features include efficient communication with web servers for prediction of N-terminal signal peptides and GPI modification sites, sequence annotation by querying hmmscan, GO enrichment based on predicted pfam domains, and the ability to classify prototypical HRGPs. 

ragp represents the first implementation of a HRGP mining workflow in the R statistical language. It implements common strategies for finding and classifying HRGP sequences along with an optional step where proline hydroxylation is estimated which leads to increased sensitivity and specificity of the filtered sequences. Since R is one of the leading bioinformatics platforms, the filtered sequences can be further analyzed by many specialized packages using the same environment.
PB  - Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad
C3  - Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89
T1  - ragp: An R toolbox for mining Hydroxyproline rich glycoproteins
SP  - 89
UR  - https://hdl.handle.net/21.15107/rcub_ibiss_4341
ER  - 

@conference{
author = "Paunović, Danijela and Bogdanović, Milica and Todorović, Slađana and Simonović, Ana and Dragićević, Milan",
year = "2018",
abstract = "Plant Hydroxyproline rich glycoproteins (HGRPs) comprise a highly diverse family of cell wall macromolecules, involved in a wide array of physiological functions such as cell expansion, somatic embryogenesis, self-incompatibility, signaling and pathogen responses. Due to biased amino acid composition, abundant in disorder promoting residues, HRGPs are intrinsically disordered proteins. The lack of a stable structure lessens the sequence constraints imposed on these proteins and hampers efforts for homology based identification. Current mining approaches, based on identifying sequences with characteristic motifs and biased amino acid composition, are limited to prototypical sequences.

Herby we present ragp, an R package for HGRP mining with a pipeline which emphasizes finding chimeric and short HRGP’s which is especially useful for identification of arabinogalactan proteins. The ragp pipeline exploits one of HGRP key features, the presence of hydroxyprolines which represent glycosylation sites. These sites are identified using a gradient boosting model trained on plant sequences with experimentally determined hydroxyprolines, based on the local (21-mer) sequence around the target prolines. The model was validated on a set of sequences which were not used during the model building, as well as by using several resampling approaches. Apart from prediction of proline hydroxylation main ragp features include efficient communication with web servers for prediction of N-terminal signal peptides and GPI modification sites, sequence annotation by querying hmmscan, GO enrichment based on predicted pfam domains, and the ability to classify prototypical HRGPs. 

ragp represents the first implementation of a HRGP mining workflow in the R statistical language. It implements common strategies for finding and classifying HRGP sequences along with an optional step where proline hydroxylation is estimated which leads to increased sensitivity and specificity of the filtered sequences. Since R is one of the leading bioinformatics platforms, the filtered sequences can be further analyzed by many specialized packages using the same environment.",
publisher = "Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad",
journal = "Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89",
title = "ragp: An R toolbox for mining Hydroxyproline rich glycoproteins",
pages = "89",
url = "https://hdl.handle.net/21.15107/rcub_ibiss_4341"
}

Paunović, D., Bogdanović, M., Todorović, S., Simonović, A.,& Dragićević, M.. (2018). ragp: An R toolbox for mining Hydroxyproline rich glycoproteins. in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89
Novi Sad: Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad., 89.
https://hdl.handle.net/21.15107/rcub_ibiss_4341

Paunović D, Bogdanović M, Todorović S, Simonović A, Dragićević M. ragp: An R toolbox for mining Hydroxyproline rich glycoproteins. in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89. 2018;:89.
https://hdl.handle.net/21.15107/rcub_ibiss_4341 .

Paunović, Danijela, Bogdanović, Milica, Todorović, Slađana, Simonović, Ana, Dragićević, Milan, "ragp: An R toolbox for mining Hydroxyproline rich glycoproteins" in Biologia Serbica: BELBI2018, 18. - 22 June 2018., Belgrade, Serbia, Book of Abstracts, p89 (2018):89,
https://hdl.handle.net/21.15107/rcub_ibiss_4341 .